From cannataro at unicz.it Thu Apr 1 11:22:12 2010 From: cannataro at unicz.it (Mario Cannataro) Date: Thu, 1 Apr 2010 17:22:12 +0200 (CEST) Subject: [BiO BB] ACM-BCB 2010 - 1st Workshop on Protein-protein interaction data: management, querying and analysis In-Reply-To: <72c4ffffd120634dccdde189790e4eb7.squirrel@email.unicz.it> References: <72c4ffffd120634dccdde189790e4eb7.squirrel@email.unicz.it> Message-ID: <178864d98c7923a3becd469c56f2db5f.squirrel@email.unicz.it> I apologize for any cross-posting of this announcement. ===================================================================== ACM International Conference on Bioinformatics and Computational Biology August 2-4, 2010. Niagara Falls, New York, U.S.A. 1st Workshop on Protein-protein interaction data: management, querying and analysis http://bioingegneria.unicz.it/~guzzi/ACM-BCB2010 Submission deadline extended to April 15, 2010. CALL FOR PAPERS Goals Biological macromolecules, such as proteins, play their role by interacting among them. Nowadays, many biochemical interactions among biological macromolecules are known, thanks to the application of different experimental platforms using different technologies, such as Yeast2Hybrid, Mass Spectrometry, etc. Results of such interactions may be stored in databases originating a knowledge base for biochemical reactions among known macromolecules. A key area in such field is the study of the interactions among proteins, especially within a cell. Currently, different experiments have lead to the accumulation of a large amount of data about proteins, also referred as Protein-Protein Interaction (PPI) data. Nevertheless, as the analysis of single protein structure requires large computational efforts, also analysing protein to protein interactions requires algorithms and software platforms for the modeling, management and analysis of PPI data. Moreover, thanks to such an interest in interactions, representing a large base of protein to protein interactions may generate a very large network, referred to as Protein Interaction Network (PIN), that codes biochemical and spatial relations among proteins. The analysis of such networks allows to discover new knowledge about biological functionalities. PINs can be represented by using (direct) graphs where nodes are associated to proteins, and edges represent interactions among proteins. Once that an interaction network is modeled by using a graph, the study of biological properties can be done using graph-based algorithms and associating biological properties of the modeled PPI to the topological properties of the underlying graph. In recent years many research efforts have produced different databases for storing interactions (PPI databases), as well as many algorithms for analyzing PINs and software tool for their visualization. Analysis algorithms can be grouped in three main classes: (i) algorithms that predict protein complexes, (ii) algorithms used for the extraction of functional modules (e.g. pathways), and (iii) algorithms for the alignment of PPI networks (e.g. belonging to different organisms). Nevertheless, many research problems are still open such as: the integration of existing databases in a large map of interaction, the introduction of semantic technologies to manage, query and analyze data, the introduction of novel models able to represent the spatio-temporal variation of interactome, the integration of PPI information with biochemical pathways, gene (regulatory) pathways, and transcriptomics. This Workshop is designed to bring together computer scientists, biologists and clinicians for exploring the current state-of-the-art research taking place in all aspects of interactomics, from basic science to clinical practice. The workshop intends to provide a forum for the presentation oforiginal research, valuable software tools (basic algorithms, modelling, analysis, and visualization tools, databases), and clinical fallouts, on topics of importance to interactomics. TOPICS OF INTEREST The topics of interest will include but will be not limited to: Data management and querying in Interactomics Data management and analysis in Interactomics Data models and integration for interactomics Querying and retrieval of PPI ?data Semantic web technologies for Interactomics Parallel and Grid-based methods for interactomics Algorithms and software tools for Interactomics Computational methods for Interactomics Novel interaction identification Protein interaction prediction Alignment of PINs Applications of Data Mining, Neural Networks, Soft Computing for interactomics Exploration and visualization of PPI ?data Interactomics and biomedical research Biomarker discovery (identification of molecular targets for early detection, prognosis and treatment of diseases Integration and analysis of genomics, proteomic, and interactomics data for medical applications IMPORTANT DATES * Submission deadline: Extended to April 15, 2010. * Author notification: April 30, 2010 * Workshop Data August 2, 2010 PAPER SUBMISSION AND PUBLICATION ACM-BCB invites authors to submit papers using the link. By submitting your paper to ACM-BCB, you implicitly state that the paper is based on your own original research and that it was not and will not be submitted elsewhere. Papers should not exceed 8 pages in ACM template on 8.5 x 11 inch paper (see ACM templates). All submitted papers should be written in English. Submission implies the willingness of at least one of the authors to register and present the work associated with the paper submitted. All submitted papers will be reviewed by ACM-BCB?s technical program committee. All accepted papers of registered authors will be included in the proceedings published by ACM digital libraries. Selected papers will be invited to adapt their papers for their publication in several journals. JOURNAL SPECIAL ISSUE At the end of the workshop, we plan to invite the best 4-6 papers of the workshop for a special section on an international journal. WORKSHOP ORGANIZERS Wokshop Chair: Pietro Hiram Guzzi, University Magna Graecia of Catanzaro, Italy General Chair: Mario Cannataro, University Magna Gr?cia of Catanzaro, Italy Publicity Chair: Pierangelo Veltri, University Magna Graecia of Catanzaro, Italy PROGRAM COMMITTEE (TO BE CONFIRMED) Alejanda Gonzales Beltran, University College of London, UK Giovanni Ciriello, University of Padova, Italy Fabrizio Silvestri, ISTI-CNR, Italy **************************************** New book release Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine, and Healthcare ISBN: 978-1-60566-374-6; 1,050 pp; May 2009 Published under Medical Information Science Reference an imprint of IGI Global http://www.igi-global.com/reference/details.asp?id=34292 Edited by: Mario Cannataro, University Magna Graecia of Catanzaro, Italy **************************************** Prof. Mario Cannataro, Informatics and Biomedical Engineering, University "Magna Gr?cia" of Catanzaro, Viale Europa (Localit? Germaneto), 88100 CATANZARO, ITALY, Tel: 0961-369 4100, Fax: 0961-369 4073/4090, Email: cannataro at unicz.it, Web: http://bioingegneria.unicz.it/~cannataro/ **************************************** From hlapp at gmx.net Sat Apr 3 21:47:08 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 3 Apr 2010 21:47:08 -0400 Subject: [BiO BB] Reminder: Deadline for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <72565973-CFD6-4EB6-8BDE-4A0981857947@gmx.net> This is a reminder that the deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) is Thursday, April 8, 2010, which less than 1 week away. Please see http://bit.ly/iEvoBio_CfA for the full Call for Abstracts and author instructions. As another reminder, full talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Lightning talks (5 mins long), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of-a-Feather gatherings. The Call for Challenge entries is also open (see http://ievobio.org/ challenge.html). Tentative submission deadlines are listed on the conference website (http://ievobio.org/program.html#dates). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is an announcment-only Google group at http://groups.google.com/group/ievobio-announce . You can use the group's RSS feed (see above URL), or join the group to receive announcements by email. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) From hlapp at gmx.net Mon Apr 5 18:47:29 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 5 Apr 2010 18:47:29 -0400 Subject: [BiO BB] Student application deadline approaching for Google Summer of Code Message-ID: <3872C81C-A059-4EA4-B448-9E4731BC62DF@gmx.net> Reminder: Student applications are due by April 9, 19:00 UTC (3pm EDT, 12pm PDT, 21:00 CEST), which is only a few days away. PHYLOINFORMATICS SUMMER OF CODE 2010 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). NESCent is particularly targeting students interested in both evolutionary biology and software development. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Full details about the 2010 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2010 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2010/faqs --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org From dan.bolser at gmail.com Tue Apr 6 03:48:46 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 6 Apr 2010 08:48:46 +0100 Subject: [BiO BB] Fwd: [CD-HIT] Fwd: CD-HIT Support Request In-Reply-To: References: <4B99E901.2090600@i-a-inc.com> Message-ID: ---------- Forwarded message ---------- From: Limin Fu Date: 5 April 2010 19:24 Subject: Re: [CD-HIT] Fwd: [BiO BB] CD-HIT Support Request To: Dan Bolser Cc: cd-hit-l at bioinformatics.org Hi, The warnings from perl scripts are harmless. The critical errors are results of improper command line arguments.?cd_hit_2d.exe is supposed to work on two sequence datasets of fasta format, to cluster one dataset against the other. In this error report, *.clstr files are used as input files, which contain no sequence data, that's the cause of the errors. Regards, Limin On Sun, Apr 4, 2010 at 3:20 PM, Dan Bolser wrote: > > ---------- Forwarded message ---------- > From: Silas Labedo > Date: 12 March 2010 07:10 > Subject: [BiO BB] CD-HIT Support Request > To: bbb at bioinformatics.org, biodevelopers at bioinformatics.org > Cc: Edwin Mulwa , Patrick Njuguna > Njogu , "gsaxena at integratedanalysisinc.com" > > > > Hi Everyone, > > I am writing a clustering program in java that calls cd-hit for New, > Incremental, and Hierarchical clustering. The program works fine for > New clustering, however when I attempt to call cd-hit from within the > java code for Incremental clustering, I get errors. The error logs are > attached below. 3 different errors occured that I don't understand and > are the reason for which I am seeking your assistance. > > This error occurred when trying to execute cd-hit for hierarchical > clustering from the linux command prompt. > **************************************************************************************** > [root at ip-10-194-215-223 cd-hit]# ./psi-cd-hit-local.pl -i > hierarchical93 -o hierarchical90 -c 0.90 > Name "main::formatdb_no" used only once: possible typo at > ./psi-cd-hit-local.pl line 1712. > Name "main::known_singles" used only once: possible typo at > ./psi-cd-hit-local.pl line 1873. > Name "main::longest_ide" used only once: possible typo at > ./psi-cd-hit-local.pl line 966. > Name "main::known_single" used only once: possible typo at > ./psi-cd-hit-local.pl line 1873. > [root at ip-10-194-215-223 cd-hit]# > > > [root at ip-10-194-215-223 cd-hit]# perl psi-cd-hit.pl -i hierarchical93 > -o hierarchical90 -c 0.3 > Name "main::reformat_seg" used only once: possible typo at > psi-cd-hit.pl line 65. > Name "main::restart_seg" used only once: possible typo at psi-cd-hit.pl line 62. > Can't exec "formatdb": No such file or directory at > .//psi-cd-hit-local.pl line 1723. > Can not formatdb at .//psi-cd-hit-local.pl line 1724. > [root at ip-10-194-215-223 cd-hit]# vi hierarchical90.log > [root at ip-10-194-215-223 cd-hit]# vi hierarchical90.out > [root at ip-10-194-215-223 cd-hit]# > > > The following outputs and subsequent errors occurred during > incremental clustering executed from within a java code. > **************************************************************************************** > Cluster CMD: ? ? ? ? C:\cd-hit-windows\cd_hit_2d.exe -i "C:/cluster > files/unipath_2010-3-9.clstr" -i2 "c:/cluster > files/unipath_2010-3-9.fasta" -o "C:/cluster files/unipath_2010-3-9" > -c 0.9 -n 5 -d 50 > > Mar 9, 2010 6:55:31 AM Here is the standard output of the command: > > total seq in db1: 0 > total seq in db2: 15732 > longest and shortest : 0 and 99999999 > Total letters: 0 > Mar 9, 2010 6:55:57 AM Process Exit Value : 1 > Mar 9, 2010 6:55:57 AM Here is the standard error of the command (if any): > > > Fatal Error > Memory > > Program halted !! > > ************************************************************************************** > Cluster CMD: ? ? ? ? C:\cd-hit-windows\cd_hit_2d.exe -i "C:/cluster > files/clusteroutput.clstr" -i2 "c:/cluster files/aric_2010-3-10.fasta" > -o "C:/cluster files/aric_2010-3-10" -c 0.9 -n 5 -d 50 > > Mar 10, 2010 6:51:01 AM Here is the standard output of the command: > > total seq in db1: 79 > total seq in db2: 4776 > longest and shortest : 48 and 11 > Total letters: 1061 > Sequences have been sorted > longest and shortest : 34350 and 11 > Total letters: 3167574 > compute index table for first database > Reading swap > Comparing with SEG 0 > ..........1000 compared ? ? ? ?0 clustered > ..........2000 compared ? ? ? ?0 clustered > ..........3000 compared ? ? ? ?0 clustered > ..........4000 compared ? ? ? ?0 clustered > ....... > 4776 compared ? ? ? ?0 clustered > writing non-redundant sequences from db2 > writing clustering information > program completed ! > > Total CPU time 103 > Mar 10, 2010 6:51:23 AM Process Exit Value : 0 > Mar 10, 2010 6:51:23 AM Here is the standard error of the command (if any): > > > The attached fasta file was generated along with the last part of the > output/error log. The contents of the fasta file are very un-familiar > and I would be very grateful if someone can help me understand it. > Thanks you all. > Regards. > > >Cluster 0 > 0 ? ? ? 56aa, >Cluster 498... * > >Cluster 1 > 0 ? ? ? 49aa, >Cluster 6436... * > >Cluster 2 > 0 ? ? ? 40aa, >Cluster 1087... * > >Cluster 3 > 0 ? ? ? 40aa, >Cluster 7998... * > >Cluster 4 > 0 ? ? ? 39aa, >Cluster 6718... * > >Cluster 5 > 0 ? ? ? 38aa, >Cluster 1072... * > >Cluster 6 > 0 ? ? ? 35aa, >Cluster 14402... * > >Cluster 7 > 0 ? ? ? 34aa, >Cluster 8584... * > >Cluster 8 > 0 ? ? ? 29aa, >Cluster 1243... * > >Cluster 9 > 0 ? ? ? 29aa, >Cluster 3934... * > >Cluster 10 > 0 ? ? ? 27aa, >Cluster 1175... * > >Cluster 11 > 0 ? ? ? 26aa, >Cluster 2224... * > >Cluster 12 > 0 ? ? ? 26aa, >Cluster 2997... * > >Cluster 13 > 0 ? ? ? 26aa, >Cluster 13025... * > >Cluster 14 > 0 ? ? ? 25aa, >Cluster 70... * > >Cluster 15 > 0 ? ? ? 25aa, >Cluster 3729... * > >Cluster 16 > 0 ? ? ? 24aa, >Cluster 3642... * > >Cluster 17 > 0 ? ? ? 24aa, >Cluster 7403... * > >Cluster 18 > 0 ? ? ? 22aa, >Cluster 371... * > >Cluster 19 > 0 ? ? ? 22aa, >Cluster 942... * > >Cluster 20 > 0 ? ? ? 22aa, >Cluster 1057... * > >Cluster 21 > 0 ? ? ? 22aa, >Cluster 4995... * > >Cluster 22 > 0 ? ? ? 22aa, >Cluster 11970... * > >Cluster 23 > 0 ? ? ? 21aa, >Cluster 1454... * > >Cluster 24 > 0 ? ? ? 21aa, >Cluster 6057... * > >Cluster 25 > 0 ? ? ? 21aa, >Cluster 6809... * > >Cluster 26 > 0 ? ? ? 21aa, >Cluster 10858... * > >Cluster 27 > 0 ? ? ? 21aa, >Cluster 13091... * > >Cluster 28 > 0 ? ? ? 21aa, >Cluster 13503... * > >Cluster 29 > 0 ? ? ? 20aa, >Cluster 418... * > >Cluster 30 > 0 ? ? ? 20aa, >Cluster 918... * > >Cluster 31 > 0 ? ? ? 20aa, >Cluster 1299... * > >Cluster 32 > 0 ? ? ? 20aa, >Cluster 1436... * > >Cluster 33 > 0 ? ? ? 20aa, >Cluster 4225... * > >Cluster 34 > 0 ? ? ? 20aa, >Cluster 7553... * > >Cluster 35 > 0 ? ? ? 20aa, >Cluster 7894... * > >Cluster 36 > 0 ? ? ? 19aa, >Cluster 123... * > >Cluster 37 > 0 ? ? ? 19aa, >Cluster 529... * > >Cluster 38 > 0 ? ? ? 19aa, >Cluster 633... * > >Cluster 39 > 0 ? ? ? 19aa, >Cluster 861... * > >Cluster 40 > 0 ? ? ? 19aa, >Cluster 890... * > >Cluster 41 > 0 ? ? ? 19aa, >Cluster 1519... * > >Cluster 42 > 0 ? ? ? 19aa, >Cluster 2298... * > >Cluster 43 > 0 ? ? ? 19aa, >Cluster 8244... * > >Cluster 44 > 0 ? ? ? 19aa, >Cluster 8906... * > >Cluster 45 > 0 ? ? ? 18aa, >Cluster 2199... * > >Cluster 46 > 0 ? ? ? 18aa, >Cluster 2271... * > >Cluster 47 > 0 ? ? ? 18aa, >Cluster 5824... * > >Cluster 48 > 0 ? ? ? 18aa, >Cluster 5961... * > >Cluster 49 > 0 ? ? ? 18aa, >Cluster 6518... * > >Cluster 50 > 0 ? ? ? 18aa, >Cluster 7567... * > >Cluster 51 > 0 ? ? ? 18aa, >Cluster 10920... * > >Cluster 52 > 0 ? ? ? 18aa, >Cluster 11850... * > >Cluster 53 > 0 ? ? ? 18aa, >Cluster 12368... * > >Cluster 54 > 0 ? ? ? 17aa, >Cluster 279... * > >Cluster 55 > 0 ? ? ? 17aa, >Cluster 780... * > >Cluster 56 > 0 ? ? ? 17aa, >Cluster 3123... * > >Cluster 57 > 0 ? ? ? 17aa, >Cluster 4123... * > >Cluster 58 > 0 ? ? ? 17aa, >Cluster 9534... * > >Cluster 59 > 0 ? ? ? 17aa, >Cluster 9544... * > >Cluster 60 > 0 ? ? ? 17aa, >Cluster 11848... * > >Cluster 61 > 0 ? ? ? 16aa, >Cluster 319... * > >Cluster 62 > 0 ? ? ? 16aa, >Cluster 1228... * > >Cluster 63 > 0 ? ? ? 16aa, >Cluster 4469... * > >Cluster 64 > 0 ? ? ? 16aa, >Cluster 7761... * > >Cluster 65 > 0 ? ? ? 15aa, >Cluster 2470... * > >Cluster 66 > 0 ? ? ? 15aa, >Cluster 5485... * > >Cluster 67 > 0 ? ? ? 15aa, >Cluster 9036... * > >Cluster 68 > 0 ? ? ? 14aa, >Cluster 16... * > >Cluster 69 > 0 ? ? ? 14aa, >Cluster 198... * > >Cluster 70 > 0 ? ? ? 14aa, >Cluster 252... * > >Cluster 71 > 0 ? ? ? 14aa, >Cluster 292... * > >Cluster 72 > 0 ? ? ? 14aa, >Cluster 364... * > >Cluster 73 > 0 ? ? ? 14aa, >Cluster 657... * > >Cluster 74 > 0 ? ? ? 14aa, >Cluster 670... * > >Cluster 75 > 0 ? ? ? 14aa, >Cluster 770... * > >Cluster 76 > 0 ? ? ? 14aa, >Cluster 869... * > >Cluster 77 > 0 ? ? ? 14aa, >Cluster 900... * > >Cluster 78 > 0 ? ? ? 14aa, >Cluster 962... * > >Cluster 79 > 0 ? ? ? 14aa, >Cluster 1137... * > >Cluster 80 > 0 ? ? ? 14aa, >Cluster 1165... * > >Cluster 81 > 0 ? ? ? 14aa, >Cluster 1230... * > >Cluster 82 > 0 ? ? ? 14aa, >Cluster 1273... * > >Cluster 83 > 0 ? ? ? 14aa, >Cluster 1659... * > >Cluster 84 > 0 ? ? ? 14aa, >Cluster 2038... * > >Cluster 85 > 0 ? ? ? 14aa, >Cluster 2318... * > >Cluster 86 > 0 ? ? ? 14aa, >Cluster 2432... * > >Cluster 87 > 0 ? ? ? 14aa, >Cluster 2651... * > >Cluster 88 > 0 ? ? ? 14aa, >Cluster 2745... * > >Cluster 89 > 0 ? ? ? 14aa, >Cluster 2767... * > >Cluster 90 > 0 ? ? ? 14aa, >Cluster 2874... * > >Cluster 91 > 0 ? ? ? 14aa, >Cluster 2904... * > >Cluster 92 > 0 ? ? ? 14aa, >Cluster 3079... * > >Cluster 93 > 0 ? ? ? 14aa, >Cluster 3091... * > >Cluster 94 > 0 ? ? ? 14aa, >Cluster 3354... * > >Cluster 95 > 0 ? ? ? 14aa, >Cluster 3400... * > >Cluster 96 > 0 ? ? ? 14aa, >Cluster 3565... * > >Cluster 97 > 0 ? ? ? 14aa, >Cluster 3884... * > >Cluster 98 > 0 ? ? ? 14aa, >Cluster 3987... * > >Cluster 99 > 0 ? ? ? 14aa, >Cluster 4079... * > >Cluster 100 > 0 ? ? ? 14aa, >Cluster 4244... * > >Cluster 101 > 0 ? ? ? 14aa, >Cluster 4350... * > >Cluster 102 > 0 ? ? ? 14aa, >Cluster 4593... * > >Cluster 103 > 0 ? ? ? 14aa, >Cluster 4601... * > >Cluster 104 > 0 ? ? ? 14aa, >Cluster 4880... * > >Cluster 105 > 0 ? ? ? 14aa, >Cluster 5149... * > >Cluster 106 > 0 ? ? ? 14aa, >Cluster 5329... * > >Cluster 107 > 0 ? ? ? 14aa, >Cluster 5677... * > >Cluster 108 > 0 ? ? ? 14aa, >Cluster 5857... * > >Cluster 109 > 0 ? ? ? 14aa, >Cluster 6106... * > >Cluster 110 > 0 ? ? ? 14aa, >Cluster 6232... * > >Cluster 111 > 0 ? ? ? 14aa, >Cluster 6306... * > >Cluster 112 > 0 ? ? ? 14aa, >Cluster 6349... * > >Cluster 113 > 0 ? ? ? 14aa, >Cluster 6355... * > >Cluster 114 > 0 ? ? ? 14aa, >Cluster 6630... * > >Cluster 115 > 0 ? ? ? 14aa, >Cluster 6805... * > >Cluster 116 > 0 ? ? ? 14aa, >Cluster 9161... * > >Cluster 117 > 0 ? ? ? 14aa, >Cluster 9297... * > >Cluster 118 > 0 ? ? ? 14aa, >Cluster 9795... * > >Cluster 119 > 0 ? ? ? 14aa, >Cluster 9942... * > >Cluster 120 > 0 ? ? ? 14aa, >Cluster 10169... * > >Cluster 121 > 0 ? ? ? 14aa, >Cluster 10709... * > >Cluster 122 > 0 ? ? ? 14aa, >Cluster 10761... * > >Cluster 123 > 0 ? ? ? 14aa, >Cluster 11147... * > >Cluster 124 > 0 ? ? ? 14aa, >Cluster 11626... * > >Cluster 125 > 0 ? ? ? 14aa, >Cluster 11637... * > >Cluster 126 > 0 ? ? ? 14aa, >Cluster 13122... * > >Cluster 127 > 0 ? ? ? 14aa, >Cluster 13790... * > >Cluster 128 > 0 ? ? ? 14aa, >Cluster 14731... * > >Cluster 129 > 0 ? ? ? 13aa, >Cluster 2... * > >Cluster 130 > 0 ? ? ? 13aa, >Cluster 8... * > >Cluster 131 > 0 ? ? ? 13aa, >Cluster 100... * > >Cluster 132 > 0 ? ? ? 13aa, >Cluster 109... * > >Cluster 133 > 0 ? ? ? 13aa, >Cluster 121... * > >Cluster 134 > 0 ? ? ? 13aa, >Cluster 136... * > >Cluster 135 > 0 ? ? ? 13aa, >Cluster 167... * > >Cluster 136 > 0 ? ? ? 13aa, >Cluster 176... * > >Cluster 137 > 0 ? ? ? 13aa, >Cluster 196... * > >Cluster 138 > 0 ? ? ? 13aa, >Cluster 231... * > >Cluster 139 > 0 ? ? ? 13aa, >Cluster 232... * > >Cluster 140 > 0 ? ? ? 13aa, >Cluster 277... * > >Cluster 141 > 0 ? ? ? 13aa, >Cluster 310... * > >Cluster 142 > 0 ? ? ? 13aa, >Cluster 323... * > >Cluster 143 > 0 ? ? ? 13aa, >Cluster 347... * > >Cluster 144 > 0 ? ? ? 13aa, >Cluster 392... * > >Cluster 145 > 0 ? ? ? 13aa, >Cluster 420... * > >Cluster 146 > 0 ? ? ? 13aa, >Cluster 431... * > >Cluster 147 > 0 ? ? ? 13aa, >Cluster 460... * > >Cluster 148 > 0 ? ? ? 13aa, >Cluster 520... * > >Cluster 149 > 0 ? ? ? 13aa, >Cluster 573... * > >Cluster 150 > 0 ? ? ? 13aa, >Cluster 590... * > >Cluster 151 > 0 ? ? ? 13aa, >Cluster 594... * > >Cluster 152 > 0 ? ? ? 13aa, >Cluster 618... * > >Cluster 153 > 0 ? ? ? 13aa, >Cluster 688... * > >Cluster 154 > 0 ? ? ? 13aa, >Cluster 803... * > >Cluster 155 > 0 ? ? ? 13aa, >Cluster 805... * > >Cluster 156 > 0 ? ? ? 13aa, >Cluster 815... * > >Cluster 157 > 0 ? ? ? 13aa, >Cluster 832... * > >Cluster 158 > 0 ? ? ? 13aa, >Cluster 837... * > >Cluster 159 > 0 ? ? ? 13aa, >Cluster 913... * > >Cluster 160 > 0 ? ? ? 13aa, >Cluster 940... * > >Cluster 161 > 0 ? ? ? 13aa, >Cluster 945... * > >Cluster 162 > 0 ? ? ? 13aa, >Cluster 970... * > >Cluster 163 > 0 ? ? ? 13aa, >Cluster 1013... * > >Cluster 164 > 0 ? ? ? 13aa, >Cluster 1034... * > >Cluster 165 > 0 ? ? ? 13aa, >Cluster 1035... * > >Cluster 166 > 0 ? ? ? 13aa, >Cluster 1086... * > >Cluster 167 > 0 ? ? ? 13aa, >Cluster 1151... * > >Cluster 168 > 0 ? ? ? 13aa, >Cluster 1162... * > >Cluster 169 > 0 ? ? ? 13aa, >Cluster 1218... * > >Cluster 170 > 0 ? ? ? 13aa, >Cluster 1253... * > >Cluster 171 > 0 ? ? ? 13aa, >Cluster 1265... * > >Cluster 172 > 0 ? ? ? 13aa, >Cluster 1341... * > >Cluster 173 > 0 ? ? ? 13aa, >Cluster 1350... * > >Cluster 174 > 0 ? ? ? 13aa, >Cluster 1352... * > >Cluster 175 > 0 ? ? ? 13aa, >Cluster 1357... * > >Cluster 176 > 0 ? ? ? 13aa, >Cluster 1443... * > >Cluster 177 > 0 ? ? ? 13aa, >Cluster 1499... * > >Cluster 178 > 0 ? ? ? 13aa, >Cluster 1653... * > >Cluster 179 > 0 ? ? ? 13aa, >Cluster 1806... * > >Cluster 180 > 0 ? ? ? 13aa, >Cluster 1861... * > >Cluster 181 > 0 ? ? ? 13aa, >Cluster 1893... * > >Cluster 182 > 0 ? ? ? 13aa, >Cluster 1905... * > >Cluster 183 > 0 ? ? ? 13aa, >Cluster 1927... * > >Cluster 184 > 0 ? ? ? 13aa, >Cluster 1942... * > >Cluster 185 > 0 ? ? ? 13aa, >Cluster 2079... * > >Cluster 186 > 0 ? ? ? 13aa, >Cluster 2313... * > >Cluster 187 > 0 ? ? ? 13aa, >Cluster 2320... * > >Cluster 188 > 0 ? ? ? 13aa, >Cluster 2332... * > >Cluster 189 > 0 ? ? ? 13aa, >Cluster 2381... * > >Cluster 190 > 0 ? ? ? 13aa, >Cluster 2391... * > >Cluster 191 > 0 ? ? ? 13aa, >Cluster 2472... * > >Cluster 192 > 0 ? ? ? 13aa, >Cluster 2486... * > >Cluster 193 > 0 ? ? ? 13aa, >Cluster 2489... * > >Cluster 194 > 0 ? ? ? 13aa, >Cluster 2516... * > >Cluster 195 > 0 ? ? ? 13aa, >Cluster 2577... * > >Cluster 196 > 0 ? ? ? 13aa, >Cluster 2608... * > >Cluster 197 > 0 ? ? ? 13aa, >Cluster 2613... * > >Cluster 198 > 0 ? ? ? 13aa, >Cluster 2634... * > >Cluster 199 > 0 ? ? ? 13aa, >Cluster 2803... * > >Cluster 200 > 0 ? ? ? 13aa, >Cluster 2805... * > >Cluster 201 > 0 ? ? ? 13aa, >Cluster 2898... * > >Cluster 202 > 0 ? ? ? 13aa, >Cluster 2949... * > >Cluster 203 > 0 ? ? ? 13aa, >Cluster 2982... * > >Cluster 204 > 0 ? ? ? 13aa, >Cluster 2987... * > >Cluster 205 > 0 ? ? ? 13aa, >Cluster 3014... * > >Cluster 206 > 0 ? ? ? 13aa, >Cluster 3065... * > >Cluster 207 > 0 ? ? ? 13aa, >Cluster 3151... * > >Cluster 208 > 0 ? ? ? 13aa, >Cluster 3197... * > >Cluster 209 > 0 ? ? ? 13aa, >Cluster 3215... * > >Cluster 210 > 0 ? ? ? 13aa, >Cluster 3280... * > >Cluster 211 > 0 ? ? ? 13aa, >Cluster 3388... * > >Cluster 212 > 0 ? ? ? 13aa, >Cluster 3492... * > >Cluster 213 > 0 ? ? ? 13aa, >Cluster 3527... * > >Cluster 214 > 0 ? ? ? 13aa, >Cluster 3531... * > >Cluster 215 > 0 ? ? ? 13aa, >Cluster 3583... * > >Cluster 216 > 0 ? ? ? 13aa, >Cluster 3685... * > >Cluster 217 > 0 ? ? ? 13aa, >Cluster 3732... * > >Cluster 218 > 0 ? ? ? 13aa, >Cluster 3735... * > >Cluster 219 > 0 ? ? ? 13aa, >Cluster 3740... * > >Cluster 220 > 0 ? ? ? 13aa, >Cluster 3977... * > >Cluster 221 > 0 ? ? ? 13aa, >Cluster 4004... * > >Cluster 222 > 0 ? ? ? 13aa, >Cluster 4115... * > >Cluster 223 > 0 ? ? ? 13aa, >Cluster 4119... * > >Cluster 224 > 0 ? ? ? 13aa, >Cluster 4139... * > >Cluster 225 > 0 ? ? ? 13aa, >Cluster 4181... * > >Cluster 226 > 0 ? ? ? 13aa, >Cluster 4184... * > >Cluster 227 > 0 ? ? ? 13aa, >Cluster 4195... * > >Cluster 228 > 0 ? ? ? 13aa, >Cluster 4243... * > >Cluster 229 > 0 ? ? ? 13aa, >Cluster 4247... * > >Cluster 230 > 0 ? ? ? 13aa, >Cluster 4324... * > >Cluster 231 > 0 ? ? ? 13aa, >Cluster 4331... * > >Cluster 232 > 0 ? ? ? 13aa, >Cluster 4377... * > >Cluster 233 > 0 ? ? ? 13aa, >Cluster 4426... * > >Cluster 234 > 0 ? ? ? 13aa, >Cluster 4587... * > >Cluster 235 > 0 ? ? ? 13aa, >Cluster 4594... * > >Cluster 236 > 0 ? ? ? 13aa, >Cluster 4671... * > >Cluster 237 > 0 ? ? ? 13aa, >Cluster 4740... * > >Cluster 238 > 0 ? ? ? 13aa, >Cluster 5015... * > >Cluster 239 > 0 ? ? ? 13aa, >Cluster 5091... * > >Cluster 240 > 0 ? ? ? 13aa, >Cluster 5102... * > >Cluster 241 > 0 ? ? ? 13aa, >Cluster 5182... * > >Cluster 242 > 0 ? ? ? 13aa, >Cluster 5217... * > >Cluster 243 > 0 ? ? ? 13aa, >Cluster 5354... * > >Cluster 244 > 0 ? ? ? 13aa, >Cluster 5360... * > >Cluster 245 > 0 ? ? ? 13aa, >Cluster 5602... * > >Cluster 246 > 0 ? ? ? 13aa, >Cluster 5642... * > >Cluster 247 > 0 ? ? ? 13aa, >Cluster 5682... * > >Cluster 248 > 0 ? ? ? 13aa, >Cluster 5693... * > >Cluster 249 > 0 ? ? ? 13aa, >Cluster 5844... * > >Cluster 250 > 0 ? ? ? 13aa, >Cluster 6013... * > >Cluster 251 > 0 ? ? ? 13aa, >Cluster 6099... * > >Cluster 252 > 0 ? ? ? 13aa, >Cluster 6100... * > >Cluster 253 > 0 ? ? ? 13aa, >Cluster 6121... * > >Cluster 254 > 0 ? ? ? 13aa, >Cluster 6154... * > >Cluster 255 > 0 ? ? ? 13aa, >Cluster 6176... * > >Cluster 256 > 0 ? ? ? 13aa, >Cluster 6249... * > >Cluster 257 > 0 ? ? ? 13aa, >Cluster 6348... * > >Cluster 258 > 0 ? ? ? 13aa, >Cluster 6361... * > >Cluster 259 > 0 ? ? ? 13aa, >Cluster 6364... * > >Cluster 260 > 0 ? ? ? 13aa, >Cluster 6502... * > >Cluster 261 > 0 ? ? ? 13aa, >Cluster 6657... * > >Cluster 262 > 0 ? ? ? 13aa, >Cluster 6709... * > >Cluster 263 > 0 ? ? ? 13aa, >Cluster 6727... * > >Cluster 264 > 0 ? ? ? 13aa, >Cluster 6851... * > >Cluster 265 > 0 ? ? ? 13aa, >Cluster 6870... * > >Cluster 266 > 0 ? ? ? 13aa, >Cluster 6914... * > >Cluster 267 > 0 ? ? ? 13aa, >Cluster 7252... * > >Cluster 268 > 0 ? ? ? 13aa, >Cluster 7419... * > >Cluster 269 > 0 ? ? ? 13aa, >Cluster 7426... * > >Cluster 270 > 0 ? ? ? 13aa, >Cluster 7528... * > >Cluster 271 > 0 ? ? ? 13aa, >Cluster 7590... * > >Cluster 272 > 0 ? ? ? 13aa, >Cluster 8112... * > >Cluster 273 > 0 ? ? ? 13aa, >Cluster 8129... * > >Cluster 274 > 0 ? ? ? 13aa, >Cluster 8157... * > >Cluster 275 > 0 ? ? ? 13aa, >Cluster 8261... * > >Cluster 276 > 0 ? ? ? 13aa, >Cluster 8531... * > >Cluster 277 > 0 ? ? ? 13aa, >Cluster 8808... * > >Cluster 278 > 0 ? ? ? 13aa, >Cluster 8840... * > >Cluster 279 > 0 ? ? ? 13aa, >Cluster 8985... * > >Cluster 280 > 0 ? ? ? 13aa, >Cluster 9186... * > >Cluster 281 > 0 ? ? ? 13aa, >Cluster 9201... * > >Cluster 282 > 0 ? ? ? 13aa, >Cluster 9268... * > >Cluster 283 > 0 ? ? ? 13aa, >Cluster 9354... * > >Cluster 284 > 0 ? ? ? 13aa, >Cluster 9356... * > >Cluster 285 > 0 ? ? ? 13aa, >Cluster 9538... * > >Cluster 286 > 0 ? ? ? 13aa, >Cluster 9675... * > >Cluster 287 > 0 ? ? ? 13aa, >Cluster 9692... * > >Cluster 288 > 0 ? ? ? 13aa, >Cluster 9695... * > >Cluster 289 > 0 ? ? ? 13aa, >Cluster 9746... * > >Cluster 290 > 0 ? ? ? 13aa, >Cluster 9769... * > >Cluster 291 > 0 ? ? ? 13aa, >Cluster 9814... * > >Cluster 292 > 0 ? ? ? 13aa, >Cluster 10011... * > >Cluster 293 > 0 ? ? ? 13aa, >Cluster 10214... * > >Cluster 294 > 0 ? ? ? 13aa, >Cluster 10251... * > >Cluster 295 > 0 ? ? ? 13aa, >Cluster 10361... * > >Cluster 296 > 0 ? ? ? 13aa, >Cluster 10450... * > >Cluster 297 > 0 ? ? ? 13aa, >Cluster 10518... * > >Cluster 298 > 0 ? ? ? 13aa, >Cluster 10648... * > >Cluster 299 > 0 ? ? ? 13aa, >Cluster 10962... * > >Cluster 300 > 0 ? ? ? 13aa, >Cluster 11121... * > >Cluster 301 > 0 ? ? ? 13aa, >Cluster 11151... * > >Cluster 302 > 0 ? ? ? 13aa, >Cluster 11519... * > >Cluster 303 > 0 ? ? ? 13aa, >Cluster 11632... * > >Cluster 304 > 0 ? ? ? 13aa, >Cluster 11867... * > >Cluster 305 > 0 ? ? ? 13aa, >Cluster 11976... * > >Cluster 306 > 0 ? ? ? 13aa, >Cluster 12006... * > >Cluster 307 > 0 ? ? ? 13aa, >Cluster 12197... * > >Cluster 308 > 0 ? ? ? 13aa, >Cluster 12363... * > >Cluster 309 > 0 ? ? ? 13aa, >Cluster 13957... * > >Cluster 310 > 0 ? ? ? 12aa, >Cluster 40... * > >Cluster 311 > 0 ? ? ? 12aa, >Cluster 51... * > >Cluster 312 > 0 ? ? ? 12aa, >Cluster 59... * > >Cluster 313 > 0 ? ? ? 12aa, >Cluster 61... * > >Cluster 314 > 0 ? ? ? 12aa, >Cluster 69... * > >Cluster 315 > 0 ? ? ? 12aa, >Cluster 72... * > >Cluster 316 > 0 ? ? ? 12aa, >Cluster 111... * > >Cluster 317 > 0 ? ? ? 12aa, >Cluster 116... * > >Cluster 318 > 0 ? ? ? 12aa, >Cluster 126... * > >Cluster 319 > 0 ? ? ? 12aa, >Cluster 195... * > >Cluster 320 > 0 ? ? ? 12aa, >Cluster 283... * > >Cluster 321 > 0 ? ? ? 12aa, >Cluster 346... * > >Cluster 322 > 0 ? ? ? 12aa, >Cluster 384... * > >Cluster 323 > 0 ? ? ? 12aa, >Cluster 394... * > >Cluster 324 > 0 ? ? ? 12aa, >Cluster 406... * > >Cluster 325 > 0 ? ? ? 12aa, >Cluster 416... * > >Cluster 326 > 0 ? ? ? 12aa, >Cluster 419... * > >Cluster 327 > 0 ? ? ? 12aa, >Cluster 426... * > >Cluster 328 > 0 ? ? ? 12aa, >Cluster 489... * > >Cluster 329 > 0 ? ? ? 12aa, >Cluster 522... * > >Cluster 330 > 0 ? ? ? 12aa, >Cluster 674... * > >Cluster 331 > 0 ? ? ? 12aa, >Cluster 677... * > >Cluster 332 > 0 ? ? ? 12aa, >Cluster 808... * > >Cluster 333 > 0 ? ? ? 12aa, >Cluster 947... * > >Cluster 334 > 0 ? ? ? 12aa, >Cluster 1015... * > >Cluster 335 > 0 ? ? ? 12aa, >Cluster 1053... * > >Cluster 336 > 0 ? ? ? 12aa, >Cluster 1085... * > >Cluster 337 > 0 ? ? ? 12aa, >Cluster 1125... * > >Cluster 338 > 0 ? ? ? 12aa, >Cluster 1154... * > >Cluster 339 > 0 ? ? ? 12aa, >Cluster 1235... * > >Cluster 340 > 0 ? ? ? 12aa, >Cluster 1264... * > >Cluster 341 > 0 ? ? ? 12aa, >Cluster 1296... * > >Cluster 342 > 0 ? ? ? 12aa, >Cluster 1314... * > >Cluster 343 > 0 ? ? ? 12aa, >Cluster 1385... * > >Cluster 344 > 0 ? ? ? 12aa, >Cluster 1451... * > >Cluster 345 > 0 ? ? ? 12aa, >Cluster 1462... * > >Cluster 346 > 0 ? ? ? 12aa, >Cluster 1479... * > >Cluster 347 > 0 ? ? ? 12aa, >Cluster 1541... * > >Cluster 348 > 0 ? ? ? 12aa, >Cluster 1610... * > >Cluster 349 > 0 ? ? ? 12aa, >Cluster 1663... * > >Cluster 350 > 0 ? ? ? 12aa, >Cluster 1672... * > >Cluster 351 > 0 ? ? ? 12aa, >Cluster 1703... * > >Cluster 352 > 0 ? ? ? 12aa, >Cluster 1817... * > >Cluster 353 > 0 ? ? ? 12aa, >Cluster 1911... * > >Cluster 354 > 0 ? ? ? 12aa, >Cluster 1965... * > >Cluster 355 > 0 ? ? ? 12aa, >Cluster 2051... * > >Cluster 356 > 0 ? ? ? 12aa, >Cluster 2151... * > >Cluster 357 > 0 ? ? ? 12aa, >Cluster 2212... * > >Cluster 358 > 0 ? ? ? 12aa, >Cluster 2236... * > >Cluster 359 > 0 ? ? ? 12aa, >Cluster 2323... * > >Cluster 360 > 0 ? ? ? 12aa, >Cluster 2530... * > >Cluster 361 > 0 ? ? ? 12aa, >Cluster 2555... * > >Cluster 362 > 0 ? ? ? 12aa, >Cluster 2620... * > >Cluster 363 > 0 ? ? ? 12aa, >Cluster 2706... * > >Cluster 364 > 0 ? ? ? 12aa, >Cluster 2755... * > >Cluster 365 > 0 ? ? ? 12aa, >Cluster 2818... * > >Cluster 366 > 0 ? ? ? 12aa, >Cluster 2824... * > >Cluster 367 > 0 ? ? ? 12aa, >Cluster 2870... * > >Cluster 368 > 0 ? ? ? 12aa, >Cluster 2910... * > >Cluster 369 > 0 ? ? ? 12aa, >Cluster 3140... * > >Cluster 370 > 0 ? ? ? 12aa, >Cluster 3213... * > >Cluster 371 > 0 ? ? ? 12aa, >Cluster 3285... * > >Cluster 372 > 0 ? ? ? 12aa, >Cluster 3364... * > >Cluster 373 > 0 ? ? ? 12aa, >Cluster 3374... * > >Cluster 374 > 0 ? ? ? 12aa, >Cluster 3603... * > >Cluster 375 > 0 ? ? ? 12aa, >Cluster 3663... * > >Cluster 376 > 0 ? ? ? 12aa, >Cluster 3692... * > >Cluster 377 > 0 ? ? ? 12aa, >Cluster 3833... * > >Cluster 378 > 0 ? ? ? 12aa, >Cluster 3940... * > >Cluster 379 > 0 ? ? ? 12aa, >Cluster 4081... * > >Cluster 380 > 0 ? ? ? 12aa, >Cluster 4224... * > >Cluster 381 > 0 ? ? ? 12aa, >Cluster 4252... * > >Cluster 382 > 0 ? ? ? 12aa, >Cluster 4274... * > >Cluster 383 > 0 ? ? ? 12aa, >Cluster 4333... * > >Cluster 384 > 0 ? ? ? 12aa, >Cluster 4364... * > >Cluster 385 > 0 ? ? ? 12aa, >Cluster 4402... * > >Cluster 386 > 0 ? ? ? 12aa, >Cluster 4427... * > >Cluster 387 > 0 ? ? ? 12aa, >Cluster 4511... * > >Cluster 388 > 0 ? ? ? 12aa, >Cluster 4548... * > >Cluster 389 > 0 ? ? ? 12aa, >Cluster 4575... * > >Cluster 390 > 0 ? ? ? 12aa, >Cluster 4586... * > >Cluster 391 > 0 ? ? ? 12aa, >Cluster 4604... * > >Cluster 392 > 0 ? ? ? 12aa, >Cluster 4637... * > >Cluster 393 > 0 ? ? ? 12aa, >Cluster 5204... * > >Cluster 394 > 0 ? ? ? 12aa, >Cluster 5398... * > >Cluster 395 > 0 ? ? ? 12aa, >Cluster 5455... * > >Cluster 396 > 0 ? ? ? 12aa, >Cluster 5515... * > >Cluster 397 > 0 ? ? ? 12aa, >Cluster 5662... * > >Cluster 398 > 0 ? ? ? 12aa, >Cluster 5683... * > >Cluster 399 > 0 ? ? ? 12aa, >Cluster 5698... * > >Cluster 400 > 0 ? ? ? 12aa, >Cluster 5789... * > >Cluster 401 > 0 ? ? ? 12aa, >Cluster 5882... * > >Cluster 402 > 0 ? ? ? 12aa, >Cluster 5989... * > >Cluster 403 > 0 ? ? ? 12aa, >Cluster 6056... * > >Cluster 404 > 0 ? ? ? 12aa, >Cluster 6060... * > >Cluster 405 > 0 ? ? ? 12aa, >Cluster 6088... * > >Cluster 406 > 0 ? ? ? 12aa, >Cluster 6297... * > >Cluster 407 > 0 ? ? ? 12aa, >Cluster 6421... * > >Cluster 408 > 0 ? ? ? 12aa, >Cluster 6479... * > >Cluster 409 > 0 ? ? ? 12aa, >Cluster 6650... * > >Cluster 410 > 0 ? ? ? 12aa, >Cluster 6798... * > >Cluster 411 > 0 ? ? ? 12aa, >Cluster 6965... * > >Cluster 412 > 0 ? ? ? 12aa, >Cluster 6967... * > >Cluster 413 > 0 ? ? ? 12aa, >Cluster 7022... * > >Cluster 414 > 0 ? ? ? 12aa, >Cluster 7043... * > >Cluster 415 > 0 ? ? ? 12aa, >Cluster 7622... * > >Cluster 416 > 0 ? ? ? 12aa, >Cluster 7690... * > >Cluster 417 > 0 ? ? ? 12aa, >Cluster 7847... * > >Cluster 418 > 0 ? ? ? 12aa, >Cluster 7849... * > >Cluster 419 > 0 ? ? ? 12aa, >Cluster 7962... * > >Cluster 420 > 0 ? ? ? 12aa, >Cluster 7987... * > >Cluster 421 > 0 ? ? ? 12aa, >Cluster 8026... * > >Cluster 422 > 0 ? ? ? 12aa, >Cluster 8081... * > >Cluster 423 > 0 ? ? ? 12aa, >Cluster 8084... * > >Cluster 424 > 0 ? ? ? 12aa, >Cluster 8198... * > >Cluster 425 > 0 ? ? ? 12aa, >Cluster 8275... * > >Cluster 426 > 0 ? ? ? 12aa, >Cluster 8546... * > >Cluster 427 > 0 ? ? ? 12aa, >Cluster 8563... * > >Cluster 428 > 0 ? ? ? 12aa, >Cluster 8637... * > >Cluster 429 > 0 ? ? ? 12aa, >Cluster 8652... * > >Cluster 430 > 0 ? ? ? 12aa, >Cluster 8806... * > >Cluster 431 > 0 ? ? ? 12aa, >Cluster 8845... * > >Cluster 432 > 0 ? ? ? 12aa, >Cluster 8996... * > >Cluster 433 > 0 ? ? ? 12aa, >Cluster 9001... * > >Cluster 434 > 0 ? ? ? 12aa, >Cluster 9017... * > >Cluster 435 > 0 ? ? ? 12aa, >Cluster 9120... * > >Cluster 436 > 0 ? ? ? 12aa, >Cluster 9183... * > >Cluster 437 > 0 ? ? ? 12aa, >Cluster 9347... * > >Cluster 438 > 0 ? ? ? 12aa, >Cluster 9427... * > >Cluster 439 > 0 ? ? ? 12aa, >Cluster 9472... * > >Cluster 440 > 0 ? ? ? 12aa, >Cluster 9661... * > >Cluster 441 > 0 ? ? ? 12aa, >Cluster 9770... * > >Cluster 442 > 0 ? ? ? 12aa, >Cluster 9906... * > >Cluster 443 > 0 ? ? ? 12aa, >Cluster 9974... * > >Cluster 444 > 0 ? ? ? 12aa, >Cluster 10101... * > >Cluster 445 > 0 ? ? ? 12aa, >Cluster 10474... * > >Cluster 446 > 0 ? ? ? 12aa, >Cluster 10527... * > >Cluster 447 > 0 ? ? ? 12aa, >Cluster 10600... * > >Cluster 448 > 0 ? ? ? 12aa, >Cluster 10750... * > >Cluster 449 > 0 ? ? ? 12aa, >Cluster 10784... * > >Cluster 450 > 0 ? ? ? 12aa, >Cluster 10944... * > >Cluster 451 > 0 ? ? ? 12aa, >Cluster 10957... * > >Cluster 452 > 0 ? ? ? 12aa, >Cluster 10999... * > >Cluster 453 > 0 ? ? ? 12aa, >Cluster 11137... * > >Cluster 454 > 0 ? ? ? 12aa, >Cluster 11231... * > >Cluster 455 > 0 ? ? ? 12aa, >Cluster 11354... * > >Cluster 456 > 0 ? ? ? 12aa, >Cluster 11475... * > >Cluster 457 > 0 ? ? ? 12aa, >Cluster 11501... * > >Cluster 458 > 0 ? ? ? 12aa, >Cluster 11646... * > >Cluster 459 > 0 ? ? ? 12aa, >Cluster 11661... * > >Cluster 460 > 0 ? ? ? 12aa, >Cluster 11738... * > >Cluster 461 > 0 ? ? ? 12aa, >Cluster 11885... * > >Cluster 462 > 0 ? ? ? 12aa, >Cluster 11919... * > >Cluster 463 > 0 ? ? ? 12aa, >Cluster 12947... * > >Cluster 464 > 0 ? ? ? 12aa, >Cluster 13014... * > >Cluster 465 > 0 ? ? ? 12aa, >Cluster 13061... * > >Cluster 466 > 0 ? ? ? 12aa, >Cluster 13438... * > >Cluster 467 > 0 ? ? ? 12aa, >Cluster 13567... * > >Cluster 468 > 0 ? ? ? 12aa, >Cluster 13784... * > >Cluster 469 > 0 ? ? ? 12aa, >Cluster 14713... * > >Cluster 470 > 0 ? ? ? 11aa, >Cluster 37... * > >Cluster 471 > 0 ? ? ? 11aa, >Cluster 80... * > >Cluster 472 > 0 ? ? ? 11aa, >Cluster 115... * > >Cluster 473 > 0 ? ? ? 11aa, >Cluster 130... * > >Cluster 474 > 0 ? ? ? 11aa, >Cluster 153... * > >Cluster 475 > 0 ? ? ? 11aa, >Cluster 235... * > >Cluster 476 > 0 ? ? ? 11aa, >Cluster 275... * > >Cluster 477 > 0 ? ? ? 11aa, >Cluster 328... * > >Cluster 478 > 0 ? ? ? 11aa, >Cluster 342... * > >Cluster 479 > 0 ? ? ? 11aa, >Cluster 435... * > >Cluster 480 > 0 ? ? ? 11aa, >Cluster 438... * > >Cluster 481 > 0 ? ? ? 11aa, >Cluster 456... * > >Cluster 482 > 0 ? ? ? 11aa, >Cluster 488... * > >Cluster 483 > 0 ? ? ? 11aa, >Cluster 549... * > >Cluster 484 > 0 ? ? ? 11aa, >Cluster 552... * > >Cluster 485 > 0 ? ? ? 11aa, >Cluster 581... * > >Cluster 486 > 0 ? ? ? 11aa, >Cluster 585... * > >Cluster 487 > 0 ? ? ? 11aa, >Cluster 591... * > >Cluster 488 > 0 ? ? ? 11aa, >Cluster 624... * > >Cluster 489 > 0 ? ? ? 11aa, >Cluster 627... * > >Cluster 490 > 0 ? ? ? 11aa, >Cluster 640... * > >Cluster 491 > 0 ? ? ? 11aa, >Cluster 767... * > >Cluster 492 > 0 ? ? ? 11aa, >Cluster 774... * > >Cluster 493 > 0 ? ? ? 11aa, >Cluster 898... * > >Cluster 494 > 0 ? ? ? 11aa, >Cluster 901... * > >Cluster 495 > 0 ? ? ? 11aa, >Cluster 921... * > >Cluster 496 > 0 ? ? ? 11aa, >Cluster 948... * > >Cluster 497 > 0 ? ? ? 11aa, >Cluster 997... * > >Cluster 498 > 0 ? ? ? 11aa, >Cluster 1024... * > >Cluster 499 > 0 ? ? ? 11aa, >Cluster 1066... * > >Cluster 500 > 0 ? ? ? 11aa, >Cluster 1077... * > >Cluster 501 > 0 ? ? ? 11aa, >Cluster 1091... * > >Cluster 502 > 0 ? ? ? 11aa, >Cluster 1098... * > >Cluster 503 > 0 ? ? ? 11aa, >Cluster 1208... * > >Cluster 504 > 0 ? ? ? 11aa, >Cluster 1337... * > >Cluster 505 > 0 ? ? ? 11aa, >Cluster 1355... * > >Cluster 506 > 0 ? ? ? 11aa, >Cluster 1485... * > >Cluster 507 > 0 ? ? ? 11aa, >Cluster 1495... * > >Cluster 508 > 0 ? ? ? 11aa, >Cluster 1735... * > >Cluster 509 > 0 ? ? ? 11aa, >Cluster 1825... * > >Cluster 510 > 0 ? ? ? 11aa, >Cluster 1892... * > >Cluster 511 > 0 ? ? ? 11aa, >Cluster 1948... * > >Cluster 512 > 0 ? ? ? 11aa, >Cluster 2031... * > >Cluster 513 > 0 ? ? ? 11aa, >Cluster 2064... * > >Cluster 514 > 0 ? ? ? 11aa, >Cluster 2104... * > >Cluster 515 > 0 ? ? ? 11aa, >Cluster 2213... * > >Cluster 516 > 0 ? ? ? 11aa, >Cluster 2325... * > >Cluster 517 > 0 ? ? ? 11aa, >Cluster 2338... * > >Cluster 518 > 0 ? ? ? 11aa, >Cluster 2452... * > >Cluster 519 > 0 ? ? ? 11aa, >Cluster 2478... * > >Cluster 520 > 0 ? ? ? 11aa, >Cluster 2501... * > >Cluster 521 > 0 ? ? ? 11aa, >Cluster 2663... * > >Cluster 522 > 0 ? ? ? 11aa, >Cluster 2671... * > >Cluster 523 > 0 ? ? ? 11aa, >Cluster 2691... * > >Cluster 524 > 0 ? ? ? 11aa, >Cluster 2735... * > >Cluster 525 > 0 ? ? ? 11aa, >Cluster 2825... * > >Cluster 526 > 0 ? ? ? 11aa, >Cluster 2837... * > >Cluster 527 > 0 ? ? ? 11aa, >Cluster 2844... * > >Cluster 528 > 0 ? ? ? 11aa, >Cluster 2860... * > >Cluster 529 > 0 ? ? ? 11aa, >Cluster 2955... * > >Cluster 530 > 0 ? ? ? 11aa, >Cluster 3074... * > >Cluster 531 > 0 ? ? ? 11aa, >Cluster 3103... * > >Cluster 532 > 0 ? ? ? 11aa, >Cluster 3104... * > >Cluster 533 > 0 ? ? ? 11aa, >Cluster 3166... * > >Cluster 534 > 0 ? ? ? 11aa, >Cluster 3174... * > >Cluster 535 > 0 ? ? ? 11aa, >Cluster 3302... * > >Cluster 536 > 0 ? ? ? 11aa, >Cluster 3453... * > >Cluster 537 > 0 ? ? ? 11aa, >Cluster 3721... * > >Cluster 538 > 0 ? ? ? 11aa, >Cluster 3723... * > >Cluster 539 > 0 ? ? ? 11aa, >Cluster 3859... * > >Cluster 540 > 0 ? ? ? 11aa, >Cluster 3872... * > >Cluster 541 > 0 ? ? ? 11aa, >Cluster 3887... * > >Cluster 542 > 0 ? ? ? 11aa, >Cluster 3910... * > >Cluster 543 > 0 ? ? ? 11aa, >Cluster 3915... * > >Cluster 544 > 0 ? ? ? 11aa, >Cluster 3966... * > >Cluster 545 > 0 ? ? ? 11aa, >Cluster 4150... * > >Cluster 546 > 0 ? ? ? 11aa, >Cluster 4240... * > >Cluster 547 > 0 ? ? ? 11aa, >Cluster 4258... * > >Cluster 548 > 0 ? ? ? 11aa, >Cluster 4321... * > >Cluster 549 > 0 ? ? ? 11aa, >Cluster 4462... * > >Cluster 550 > 0 ? ? ? 11aa, >Cluster 4557... * > >Cluster 551 > 0 ? ? ? 11aa, >Cluster 4564... * > >Cluster 552 > 0 ? ? ? 11aa, >Cluster 4589... * > >Cluster 553 > 0 ? ? ? 11aa, >Cluster 4612... * > >Cluster 554 > 0 ? ? ? 11aa, >Cluster 4617... * > >Cluster 555 > 0 ? ? ? 11aa, >Cluster 4690... * > >Cluster 556 > 0 ? ? ? 11aa, >Cluster 4692... * > >Cluster 557 > 0 ? ? ? 11aa, >Cluster 4779... * > >Cluster 558 > 0 ? ? ? 11aa, >Cluster 4906... * > >Cluster 559 > 0 ? ? ? 11aa, >Cluster 5063... * > >Cluster 560 > 0 ? ? ? 11aa, >Cluster 5076... * > >Cluster 561 > 0 ? ? ? 11aa, >Cluster 5085... * > >Cluster 562 > 0 ? ? ? 11aa, >Cluster 5170... * > >Cluster 563 > 0 ? ? ? 11aa, >Cluster 5185... * > >Cluster 564 > 0 ? ? ? 11aa, >Cluster 5195... * > >Cluster 565 > 0 ? ? ? 11aa, >Cluster 5196... * > >Cluster 566 > 0 ? ? ? 11aa, >Cluster 5254... * > >Cluster 567 > 0 ? ? ? 11aa, >Cluster 5364... * > >Cluster 568 > 0 ? ? ? 11aa, >Cluster 5409... * > >Cluster 569 > 0 ? ? ? 11aa, >Cluster 5443... * > >Cluster 570 > 0 ? ? ? 11aa, >Cluster 5476... * > >Cluster 571 > 0 ? ? ? 11aa, >Cluster 5593... * > >Cluster 572 > 0 ? ? ? 11aa, >Cluster 5725... * > >Cluster 573 > 0 ? ? ? 11aa, >Cluster 5808... * > >Cluster 574 > 0 ? ? ? 11aa, >Cluster 5869... * > >Cluster 575 > 0 ? ? ? 11aa, >Cluster 5912... * > >Cluster 576 > 0 ? ? ? 11aa, >Cluster 5924... * > >Cluster 577 > 0 ? ? ? 11aa, >Cluster 6143... * > >Cluster 578 > 0 ? ? ? 11aa, >Cluster 6147... * > >Cluster 579 > 0 ? ? ? 11aa, >Cluster 6326... * > >Cluster 580 > 0 ? ? ? 11aa, >Cluster 6384... * > >Cluster 581 > 0 ? ? ? 11aa, >Cluster 6556... * > >Cluster 582 > 0 ? ? ? 11aa, >Cluster 6764... * > >Cluster 583 > 0 ? ? ? 11aa, >Cluster 6782... * > >Cluster 584 > 0 ? ? ? 11aa, >Cluster 6811... * > >Cluster 585 > 0 ? ? ? 11aa, >Cluster 6867... * > >Cluster 586 > 0 ? ? ? 11aa, >Cluster 7160... * > >Cluster 587 > 0 ? ? ? 11aa, >Cluster 7182... * > >Cluster 588 > 0 ? ? ? 11aa, >Cluster 7224... * > >Cluster 589 > 0 ? ? ? 11aa, >Cluster 7543... * > >Cluster 590 > 0 ? ? ? 11aa, >Cluster 7550... * > >Cluster 591 > 0 ? ? ? 11aa, >Cluster 7565... * > >Cluster 592 > 0 ? ? ? 11aa, >Cluster 7708... * > >Cluster 593 > 0 ? ? ? 11aa, >Cluster 7763... * > >Cluster 594 > 0 ? ? ? 11aa, >Cluster 7965... * > >Cluster 595 > 0 ? ? ? 11aa, >Cluster 7993... * > >Cluster 596 > 0 ? ? ? 11aa, >Cluster 8077... * > >Cluster 597 > 0 ? ? ? 11aa, >Cluster 8238... * > >Cluster 598 > 0 ? ? ? 11aa, >Cluster 8301... * > >Cluster 599 > 0 ? ? ? 11aa, >Cluster 8365... * > >Cluster 600 > 0 ? ? ? 11aa, >Cluster 8854... * > >Cluster 601 > 0 ? ? ? 11aa, >Cluster 9159... * > >Cluster 602 > 0 ? ? ? 11aa, >Cluster 9176... * > >Cluster 603 > 0 ? ? ? 11aa, >Cluster 9303... * > >Cluster 604 > 0 ? ? ? 11aa, >Cluster 9321... * > >Cluster 605 > 0 ? ? ? 11aa, >Cluster 9441... * > >Cluster 606 > 0 ? ? ? 11aa, >Cluster 9469... * > >Cluster 607 > 0 ? ? ? 11aa, >Cluster 9516... * > >Cluster 608 > 0 ? ? ? 11aa, >Cluster 9730... * > >Cluster 609 > 0 ? ? ? 11aa, >Cluster 9800... * > >Cluster 610 > 0 ? ? ? 11aa, >Cluster 10147... * > >Cluster 611 > 0 ? ? ? 11aa, >Cluster 10181... * > >Cluster 612 > 0 ? ? ? 11aa, >Cluster 10253... * > >Cluster 613 > 0 ? ? ? 11aa, >Cluster 10714... * > >Cluster 614 > 0 ? ? ? 11aa, >Cluster 10968... * > >Cluster 615 > 0 ? ? ? 11aa, >Cluster 11025... * > >Cluster 616 > 0 ? ? ? 11aa, >Cluster 11053... * > >Cluster 617 > 0 ? ? ? 11aa, >Cluster 11284... * > >Cluster 618 > 0 ? ? ? 11aa, >Cluster 12381... * > >Cluster 619 > 0 ? ? ? 11aa, >Cluster 12418... * > >Cluster 620 > 0 ? ? ? 11aa, >Cluster 12784... * > >Cluster 621 > 0 ? ? ? 11aa, >Cluster 13017... * > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > _______________________________________________ > CD-HIT-l mailing list > CD-HIT-l at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/cd-hit-l From hlapp at gmx.net Wed Apr 7 10:37:16 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 7 Apr 2010 10:37:16 -0400 Subject: [BiO BB] Deadline extension for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <5C62093A-685B-4EBB-BD7B-12FA78C344BE@gmx.net> The deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended by one week to Thursday, April 15, 2010. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio_CfA for the full Call for Abstracts and author instructions. We still expect to be able to notify accepted talks in time for the early registration deadline of iEvoBio (and Evolution). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) From cannataro at unicz.it Fri Apr 9 16:04:16 2010 From: cannataro at unicz.it (Mario Cannataro) Date: Fri, 9 Apr 2010 22:04:16 +0200 (CEST) Subject: [BiO BB] CBMS 2010 - 5th Special Track Computational Proteomics and Genomics In-Reply-To: <72c4ffffd120634dccdde189790e4eb7.squirrel@email.unicz.it> References: <72c4ffffd120634dccdde189790e4eb7.squirrel@email.unicz.it> Message-ID: I apologize for any cross-posting of this announcement. ===================================================================== 23rd IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS Perth, Australia, 12-15 October 2010 5th Special Track Computational Proteomics and Genomics: Data Management and Analysis http://staff.icar.cnr.it/cannataro/cbms2010 ===================================================================== * * * CALL FOR PAPERS - Deadline June 17, 2010 * * * ===================================================================== Genomics is the study of the genome, i.e. the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). Investigation of single genes, their functions and roles is becoming common practice in today's medical and biological research. Genome-wide sequencing projects have been completed for many organisms, including Homo Sapiens. Currently thousands of genes have been sequenced but still wait for any functional information to be assigned to them: this suggests that current comprehension of most biological and pathological processes is by far incomplete. As a consequence, new technological platforms that exploit the genome sequence information to explore gene function in a systematic way are evolving at an incredibly high pace, e.g. microarray. Application of the microarray technology has unveiled its enormous potential as a diagnostic support to clinical management. Recent works exploited gene expression profiling of tumor samples to define sets of genes (signatures) whose expression correlates, positively or negatively, with specific clinical features, such survival and response to therapy. Other types of massive datasets currently generated in genomics and projects include: protein expression levels measured by proteomics screenings; protein-protein interaction datasets in various organisms; protein structure data; genomic sequencing of additional organisms, comparative genomics; sequence polymorphisms in human populations, mutational analysis in human cancer and in hereditary diseases. Proteomics is a fastly developing area of biochemical investigation and regards the study of the proteins expressed in an organism or a cell. Proteomics studies include: protein identification and quantification, structural genomics, protein-to-protein interaction, post-translational modifications, and so on. In medical studies, the basic aim of proteomic analysis is the identification of specific protein patterns from cells, tissues and biological fluids related to physiological or pathological conditions (biomarker discovery). It provides a different view as compared to gene expression profiling, which does not evaluate post-transcriptional, post-translational modifications as well as protein compartimentalization and half-life changes (for instance ubiquitination and proteasome-driven degradation). All these characteristics make the protein profile much more complex but more informative compared to gene expression profiling. Several approaches have been used to perform proteomic analysis; among them, technologies based on Mass Spectrometry (MS) have revolutionized proteomics and are heavily used to make high-throughput measurements for identifying macromolecules in a specific compound. Some recent studies based on mass spectrometry, conducted at the National Institutes of Health, USA, have identified in biological samples cluster patterns that completely segregated ovarian cancer from non-cancer. These results, characterized by a high degree of sensitivity and specificity, represent an extraordinary step forward in the early detection and diagnosis of ovarian cancer and justify a prospective population-based assessment of proteomic pattern technology as a screening tool for all stages of ovarian cancer in high-risk and general populations. Similar studies performed on different types of neoplastic diseases have confirmed the importance of identification of ?molecular profiles or signatures? (either at RNA or protein level) as a powerful tool for innovative diagnostic and therapeutic approaches. Computational Proteomics is about the computational methods, algorithms, databases, and methodologies used to manage, analyze and interpret the data produced in proteomics experiments. The broad application of proteomics in different biological and medical fields, as well as the increasing resolution and precision offered by technological platforms, make the analysis of proteomics experiments difficult and error prone without efficient algorithms and easy-to-use tools. This is especially true in Mass Spectrometry-based high-throughput proteomics, where the production of huge datasets is coupled with the need of on-the-fly data analysis. The seamless integration of genomic, proteomics and clinical data, and the semantic interoperation between bioinformatics tools and health management systems, are first steps toward the so-called ?Genomic Medicine?, i.e. the combined use of genomics, proteomics, and clinical data to improve healthcare. Future Electronic Patient Records should allow the integration of genomic and proteomic data, while bioinformatics tools and databases used for genomics and proteomics studies should be able to furnish input to clinical practice, enabling the so called ?from-bench-to-bed? paradigm. This Workshop is designed to bring together computer scientists, biologists and clinicians for exploring the current state-of-the-art research taking place in all aspects of computational proteomics and genomics, from basic science to clinical practice. The workshop intends to provide a forum for the presentation of original research, valuable software tools (basic algorithms, modelling, analysis, and visualization tools, databases), and clinical fallouts, on topics of importance to computational genomics and proteomics. TOPICS OF INTEREST The topics of interest will include but will be not limited to: Data management and analysis in Computational Proteomics and Genomics o Computational methods for microarray o Computational methods for mass spectrometry o Pre-processing and analysis of microarray data o Pre-processing and analysis of mass-spectrometry data o Florescence-based methods and related image processing techniques o Peptide/protein identification o Protein structure prediction o Applications of Data Mining, Neural Networks, Soft Computing for proteomics o Software environments for proteomics and genomics workflows o Exploration and visualization of proteomic and genomics data o Data models and integration for proteomics and genomics o Querying and retrieval of proteomics and genomics data o Knowledge management, text mining and ontologies for proteomics and genomics o System biology ( protein-protein interactions, signalling networks) o Parallel and Grid-based methods for proteomics and genomics o Service Oriented approaches for Life Sciences applications o Standards in proteomics and genomics Applications of Genomics and Proteomics in Clinical Practice o Biomarker discovery (identification of molecular targets for early detection, prognosis and treatment of diseases) o Technologies and data models for phenotype, genotype and proteotype data o Integration and analysis of genomics, proteomic, and clinical data for medical applications o Application of proteomics methods in clinical practice o Advanced Electronic Patient Records o Data quality and provenance o Medical Images PAPER SUBMISSION AND PUBLICATION We invite original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Each paper must be prepared following the IEEE 2-column format and should not exceed the length of 6 (six) letter-sized pages, submitted electronically using the paper submission system prior to the submission deadline. CBMS 2010 submission web site is http://www.cbms2010.debii.curtin.edu.au All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. Please contact cannataro AT unicz DOT it for any question. IMPORTANT DATES Submission deadline for regular papers: 17 Jun 2010 Notification of acceptation: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 TRACK CO-CHAIRS: * Mario Cannataro (University ?Magna Gr?cia? of Catanzaro, Italy) * Giovanni Cuda (University ?Magna Gr?cia? of Catanzaro, Italy) * Marco Gaspari (University ?Magna Gr?cia? of Catanzaro, Italy) * Pierangelo Veltri (University ?Magna Gr?cia? of Catanzaro, Italy) PROGRAM COMMITTEE (PROVISIONAL) * Tim Clark, Harvard Medical School - MassGeneral Institute for Neurodegenerative Disease, USA * Giuseppe Di Fatta, University of Reading, UK * Cesare Furlanello, FBK - Fondazione Bruno Kessler, Italy * Christine Froidevaux, LRI-Bioinformatics Group - University Paris XI, Orsay, France * Concettina Guerra, University of Padova, Italy * Pietro Hiram Guzzi, University ?Magna Gr?cia? of Catanzaro, Italy * Hasan Jamil, Wayne State University, Michigan, USA * Ela Hunt, ETHZ, Switzerland * Maria Mirto, University of Salento, Italy * Stephen Pennington, Conway Institute, University College Dublin, Ireland * Simona Rombo, University of Calabria, Italy * Dennis Shields, Conway Institute, University College Dublin, Ireland * Roberto Tagliaferri, University of Salerno, Italy * Jason Wong, University of New South Wales, Australia From pj.siivola at luukku.com Mon Apr 12 06:15:45 2010 From: pj.siivola at luukku.com (=?ISO-8859-1?Q?p=E4ivi_siivola?=) Date: Mon, 12 Apr 2010 13:15:45 +0300 (EEST) Subject: [BiO BB] how to search genes around certain SNP Message-ID: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> Hi! I would be interested to find out genes around spesific SNPs (genes which are ~ 1 MB away from SNP or less). What would be most efficient way to do this ? Suggestions? Thanks in advance! P?ivi Rosenstr?m .................................................................... Luukku Plus -paketilla p??set eroon tila- ja turvallisuusongelmista. Hanki Luukku Plus ja helpotat el?m??si. http://www.mtv3.fi/luukku From marchywka at hotmail.com Wed Apr 14 07:35:07 2010 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 14 Apr 2010 07:35:07 -0400 Subject: [BiO BB] how to search genes around certain SNP In-Reply-To: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> Message-ID: . ---------------------------------------- > Date: Mon, 12 Apr 2010 13:15:45 +0300 > From: pj.siivola at luukku.com > To: bbb at bioinformatics.org > Subject: [BiO BB] how to search genes around certain SNP > > Hi! > > I would be interested to find out genes around spesific SNPs (genes which are ~ 1 MB away from SNP or less). What would be most efficient way to do this ? Suggestions? > You want annotated genome or you want to query a gene DB by location ( proximity to your SNP) or actually plow through DNA near your SNP? I haven't tried it but something like this may help, probably lets you play with annotated genomes and your own data, http://www.ncbi.nlm.nih.gov/projects/gbench/ I don't know if anyone answered the latter cases but you can download gene DB or genomes themselves for more efficent access and specialize the local storage format to your immediate needs ( this all takes time but if you really care about efficient usage it can produce benefits). In the past I've done similar things by requsting large junks of adjcent genome from the relevant database at ncbi. I guess efficient depends on usage however. If you do this a lot, and if you really care about efficiency, it may be faster to get a local copy of your targets genome and put into a DB of your choice. "DB" could just be a bunch of flat files and use some simple compressed format with chunk sizes that give you reaonable "random access" performance. For example, name files something like ChromoX_start_N_end_M.zip and then load/unzip the one or two that have the relevant data. Simple content specialized compression ( like changing 8 bit chars into 2( Although IIRC this has problems for placeholders for missing data, there may be other issues on which someone could comment ) may improve performance( even if you have plenty of disk space, transfer and memory acceses may be faster if the data is smaller). Does this address your need? > > Thanks in advance! > > P?ivi Rosenstr?m > _________________________________________________________________ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1 From skhadar at gmail.com Mon Apr 12 20:59:25 2010 From: skhadar at gmail.com (Khader Shameer) Date: Mon, 12 Apr 2010 17:59:25 -0700 Subject: [BiO BB] how to search genes around certain SNP In-Reply-To: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> Message-ID: Hi Paivi, I have recently asked this question at http://biostar.stackechange.com . I got an excellent answer for this (thx to Pierre) to get these via UCSC public mysql db. Check the question and answers here : http://biostar.stackexchange.com/questions/413/how-to-map-a-snp-to-a-gene-around-60kb Thanks, Shameer Khader Mayo Clinic, Rochester Campus On Mon, Apr 12, 2010 at 3:15 AM, p?ivi siivola wrote: > Hi! > > I would be interested to find out genes around spesific SNPs (genes which > are ~ 1 MB away from SNP or less). What would be most efficient way to do > this ? Suggestions? > > > Thanks in advance! > > P?ivi Rosenstr?m > > .................................................................... > Luukku Plus -paketilla p??set eroon tila- ja turvallisuusongelmista. > Hanki Luukku Plus ja helpotat el?m??si. http://www.mtv3.fi/luukku > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From ybolo001 at student.ucr.edu Mon Apr 12 23:05:04 2010 From: ybolo001 at student.ucr.edu (Eugene Bolotin) Date: Mon, 12 Apr 2010 20:05:04 -0700 Subject: [BiO BB] how to search genes around certain SNP In-Reply-To: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> Message-ID: I did this, I used a database of SNPs and positions from Refseq, and a database of gene starts and ends from Refseq. Then I cross referenced it using SQL. You can also use perl script. EB On Mon, Apr 12, 2010 at 3:15 AM, p?ivi siivola wrote: > Hi! > > I would be interested to find out genes around spesific SNPs (genes which are ~ 1 MB away from SNP or less). What would be most efficient way to do this ? ?Suggestions? > > > Thanks in advance! > > P?ivi Rosenstr?m > > .................................................................... > Luukku Plus -paketilla p??set eroon tila- ja turvallisuusongelmista. > Hanki Luukku Plus ja helpotat el?m??si. http://www.mtv3.fi/luukku > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Eugene Bolotin, Ph.D. Genetics Genomics and Bioinformatics University of California Riverside ybolo001 at student.ucr.edu Dr. Frances Sladek Lab From kry.kieslowski at gmail.com Fri Apr 16 09:35:40 2010 From: kry.kieslowski at gmail.com (Ilgar Abdullayev) Date: Fri, 16 Apr 2010 15:35:40 +0200 Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? In-Reply-To: References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com> Message-ID: <4BC867AC.1010309@gmail.com> Dear BBB forum members For my thesis, I was looking for reliable database of Human 3' UTRs. Could someone please help me for that. I would really appreciate. Thanks From x.sole at iconcologia.net Fri Apr 16 11:31:19 2010 From: x.sole at iconcologia.net (Sole Acha, Xavi) Date: Fri, 16 Apr 2010 17:31:19 +0200 Subject: [BiO BB] Opinion about Affy U219 platform Message-ID: <50805D6FBD91904D86AF433349315E42028FEE18@ICOSRVCORREO01.ICO.SCS.local> Dear all, I was wondering if anybody has successfully used Affy U219 platform for gene expression assays. How does it compare against 133 Plus2? 133 Plus2 currently seems quite outdated in terms of annotation. We're about to start a project but are not completely sure about this new array. In GEO there are no data available... maybe is too early? Bioconductor seems not to have too mcuh support for this array either. What do you think? Asking in a more general way... I know it is not an easy question, but if you were to start a microarray expression project what would you believe to be a good choice regarding the platformn quality (and price)? Thank you very much in advance! Xavi. ------ Xavier Sol? Acha Unitat de Biomarcadors i Susceptibilitat Unit of Biomarkers and Susceptibility Institut Catal? d'Oncologia // Catalan Institute of Oncology Gran Via de L'Hospitalet?199-203 08907 L'Hospitalet de Llobregat, Barcelona, Spain. Phone: +34 93 260 71 86 / +34 93 335 90 11 (ext. 3189) Fax: +34 93 260 71 88 E-mail: x.sole (at) iconcologia.net From svtrived at hotmail.com Sat Apr 17 04:04:56 2010 From: svtrived at hotmail.com (Seema Trivedi) Date: Sat, 17 Apr 2010 13:34:56 +0530 Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? In-Reply-To: <4BC867AC.1010309@gmail.com> References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com>, , <4BC867AC.1010309@gmail.com> Message-ID: Hello kieslowski Try biomart of Ensembl. choose the Homo sap. option and choose the Ensembl gene (anyway the default), on features choose the UTRs and then click results. If you have a limited number of gene list, you can paste it in the box just beneath the gene/transcript etc. option. If you find it difficult there are tutorial on the Ensembl website itself and possibly on the YouTubes as well. All the best Seema Trivedi Associate Professor Dept. of Zoology JN Vyas University Jodhpur (Raj) 342001 India > Date: Fri, 16 Apr 2010 15:35:40 +0200 > From: kry.kieslowski at gmail.com > To: bbb at bioinformatics.org > Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? > > Dear BBB forum members > > For my thesis, I was looking for reliable database of Human 3' UTRs. > Could someone please help me for that. I would really appreciate. > > Thanks > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ South Cinema This Decade http://entertainment.in.msn.com/southcinemathisdecade/ From oceanhu at 126.com Mon Apr 19 01:48:55 2010 From: oceanhu at 126.com (ocean) Date: Mon, 19 Apr 2010 13:48:55 +0800 (CST) Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? In-Reply-To: References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com>, , <4BC867AC.1010309@gmail.com> Message-ID: <6fe131b0.8534.128149cbc37.Coremail.oceanhu@126.com> Hi Kieslowski, for the 3'UTR, for my experience, i think the annotation from refseq is more accurate, and so more reliable, but it might loose some 3'UTRs which are real and annotated by Ensembl but missing in refseq. For Ensembl annotation, it's true there are many more Transcripts with annotated 3'UTR comparing with refseq anntation. which database to choose, it just depends. best, Huhaiyang CAS-MPG Partner Institute for Computational Biology (PICB) Shanghai Institutes for Biological Sciences (SIBS) Chinese Academy of Sciences (CAS) 320 Yueyang Road, Shanghai 200031, P.R.China Tel:(86)-21-54920218 ?2010-04-17?"Seema Trivedi" ??? > >Hello kieslowski > >Try biomart of Ensembl. choose the Homo sap. option and choose the Ensembl gene (anyway the default), on features choose the UTRs and then click results. If you have a limited number of gene list, you can paste it in the box just beneath the gene/transcript etc. option. If you find it difficult there are tutorial on the Ensembl website itself and possibly on the YouTubes as well. > >All the best > >Seema Trivedi >Associate Professor >Dept. of Zoology >JN Vyas University >Jodhpur (Raj) >342001 >India > > > > >> Date: Fri, 16 Apr 2010 15:35:40 +0200 >> From: kry.kieslowski at gmail.com >> To: bbb at bioinformatics.org >> Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? >> >> Dear BBB forum members >> >> For my thesis, I was looking for reliable database of Human 3' UTRs. >> Could someone please help me for that. I would really appreciate. >> >> Thanks >> >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb > >_________________________________________________________________ >South Cinema This Decade >http://entertainment.in.msn.com/southcinemathisdecade/ >_______________________________________________ >BBB mailing list >BBB at bioinformatics.org >http://www.bioinformatics.org/mailman/listinfo/bbb From x.sole at iconcologia.net Mon Apr 19 04:01:57 2010 From: x.sole at iconcologia.net (Sole Acha, Xavi) Date: Mon, 19 Apr 2010 10:01:57 +0200 Subject: [BiO BB] Opinion about Affy U219 array plates Message-ID: <50805D6FBD91904D86AF433349315E42028FEEBB@ICOSRVCORREO01.ICO.SCS.local> Dear all, I was wondering if anybody has successfully used Affy U219 platform for gene expression assays. How does it compare against the older HG U133 Plus2? Although it still seems to be the standard, 133 Plus2 currently seems quite outdated in terms of annotation (and maybe probe design?). We're about to start a gene expression project of >200 samples, but are not completely sure about this new array. In GEO there are no data available... maybe is too early? Bioconductor seems not to have too mcuh support for this array either. What do you think? Asking in a more general way... I know it is not an easy question, but if you were to start a microarray expression project what would you believe to be a good choice regarding the platform quality (and price)? Thank you very much in advance! Xavi. ------ Xavier Sol? Acha Unitat de Biomarcadors i Susceptibilitat Unit of Biomarkers and Susceptibility Institut Catal? d'Oncologia // Catalan Institute of Oncology Gran Via de L'Hospitalet?199-203 08907 L'Hospitalet de Llobregat, Barcelona, Spain. Phone: +34 93 260 71 86 / +34 93 335 90 11 (ext. 3189) Fax: +34 93 260 71 88 E-mail: x.sole (at) iconcologia.net From coolswati.srivastava1 at gmail.com Mon Apr 19 13:23:53 2010 From: coolswati.srivastava1 at gmail.com (swati srivastava) Date: Mon, 19 Apr 2010 22:53:53 +0530 Subject: [BiO BB] about virtual screening Message-ID: In my desertation i have to do virtual screening. can someone tell me about the best tool fr this and steps? I will be very thankful Swati Srivastava From mkucej at yahoo.com Mon Apr 19 16:30:52 2010 From: mkucej at yahoo.com (Martin Kucej) Date: Mon, 19 Apr 2010 13:30:52 -0700 (PDT) Subject: [BiO BB] A new lead developer sought for Biobanner.org Message-ID: <652544.92569.qm@web81306.mail.mud.yahoo.com> Dear all: Some of you may have noticed a service here at Bioinformatics.org (http://www.bioinformatics.org/banners), which provides a way for web masters to advertise their websites, provided they run a non-profit site related to biology or medicine. In its heyday, this project generated more than 800K hits per month, and was moderately successful. I started BioBanner when PHP version 3 was still around, and in recent years I have slowly moved away from this project. A lot has changed since then both in web site advertising and web-based application programming. I am writing here in hope that someone would be interested in taking over this project, improve and modernize it, and inject his/her own fresh ideas that will stimulate its growth again. I know that it is not a project about bioinformatics, but BioBanner served for many years to spread word especially about bioinformatics. I think it would be a fun side project for a any programmer who masters PHP, SQL, and Javascript, and who is also interested in promotion of science. We at Bioinformatics.Org will try to provide you with all the support we can and will be especially happy if you decided to integrate this service with BiO web site. If you are interested please contact me or president of Bioinformatics.Org, Jeff Bizzaro. Thank you. Best regards, Martin Kucej BioBanner founder From dan.bolser at gmail.com Wed Apr 21 04:02:42 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 21 Apr 2010 09:02:42 +0100 Subject: [BiO BB] about virtual screening In-Reply-To: References: Message-ID: I'm not sure, but I know there is a lot of information at ChEMBL http://www.ebi.ac.uk/chembl/ HTH, Dan. On 19 April 2010 18:23, swati srivastava wrote: > In my desertation i have to do virtual screening. > can someone tell me about the best tool fr this and steps? > I will be very thankful > > Swati Srivastava > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From skhadar at gmail.com Wed Apr 21 11:29:34 2010 From: skhadar at gmail.com (Khader Shameer) Date: Wed, 21 Apr 2010 10:29:34 -0500 Subject: [BiO BB] about virtual screening In-Reply-To: References: Message-ID: Hi Swati, If you are planning to screen a protein target for ligands with various features. You can use ChEMBL as suggested by Dan or PubChem or ZINC databases. To begin with you should have a target, some hypothesis around this protein to justify the virtual screening. Then you can download one of the small molecule libraries and perform your screen. You may try AutoDock Vina (I heard its capable of virtual screening and it is freely available) or commercial packages for insilico screening. http://vina.scripps.edu/ Trust this helps, Khader Shameer On Wed, Apr 21, 2010 at 3:02 AM, Dan Bolser wrote: > I'm not sure, but I know there is a lot of information at ChEMBL > > http://www.ebi.ac.uk/chembl/ > > > HTH, > Dan. > > On 19 April 2010 18:23, swati srivastava > wrote: > > In my desertation i have to do virtual screening. > > can someone tell me about the best tool fr this and steps? > > I will be very thankful > > > > Swati Srivastava > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From skhadar at gmail.com Wed Apr 21 11:34:05 2010 From: skhadar at gmail.com (Khader Shameer) Date: Wed, 21 Apr 2010 10:34:05 -0500 Subject: [BiO BB] about virtual screening In-Reply-To: References: Message-ID: You may check this link : lots of interesting resources http://crdd.osdd.net/qsar.php On Wed, Apr 21, 2010 at 10:29 AM, Khader Shameer wrote: > Hi Swati, > > If you are planning to screen a protein target for ligands with various > features. > You can use ChEMBL as suggested by Dan or PubChem or ZINC databases. > > To begin with you should have a target, some hypothesis around this protein > to justify the virtual screening. > Then you can download one of the small molecule libraries and perform your > screen. > > You may try AutoDock Vina (I heard its capable of virtual screening and it > is freely available) or commercial packages for insilico screening. > http://vina.scripps.edu/ > > Trust this helps, > > Khader Shameer > > On Wed, Apr 21, 2010 at 3:02 AM, Dan Bolser wrote: > >> I'm not sure, but I know there is a lot of information at ChEMBL >> >> http://www.ebi.ac.uk/chembl/ >> >> >> HTH, >> Dan. >> >> On 19 April 2010 18:23, swati srivastava >> wrote: >> > In my desertation i have to do virtual screening. >> > can someone tell me about the best tool fr this and steps? >> > I will be very thankful >> > >> > Swati Srivastava >> > >> > _______________________________________________ >> > BBB mailing list >> > BBB at bioinformatics.org >> > http://www.bioinformatics.org/mailman/listinfo/bbb >> > >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > From kondabagil at yahoo.com Wed Apr 21 15:32:44 2010 From: kondabagil at yahoo.com (kiran kondabagil) Date: Wed, 21 Apr 2010 12:32:44 -0700 (PDT) Subject: [BiO BB] Help with finding GC rich regions in Bacteriophage genomes Message-ID: <310412.455.qm@web65601.mail.ac4.yahoo.com> Hi all, I am looking for a?way or a tool to map all?the GC rich?(of given percentage say, 60% or 70% GC)?short stretches of nucleotides anywhere between 20-80 base pairs in Bacteriophage T4 and other Phage genomes.I could not find such a tool at NCBI website.?I highly appreciate?your help. Thank you so much Kiran?? From neuro.informatics.at.mbl at gmail.com Thu Apr 22 17:25:44 2010 From: neuro.informatics.at.mbl at gmail.com (Neuro Informatics) Date: Thu, 22 Apr 2010 17:25:44 -0400 Subject: [BiO BB] =?windows-1252?q?WORKSHOP_ON_CIRCUIT_=26_MOLECULAR_ARCHI?= =?windows-1252?q?TECTURE_OF_THE_VERTEBRATE_BRAIN=2C_JUNE_17_=96_29?= =?windows-1252?q?=2C_2010=2C_Application_deadline=3A_April_30=2C_2?= =?windows-1252?q?010?= Message-ID: *ANNOUNCING A NEW CSH WORKSHOP ON CIRCUIT & MOLECULAR ARCHITECTURE OF THE VERTEBRATE BRAIN* Dear Colleague: *WORKSHOP ON CIRCUIT & MOLECULAR ARCHITECTURE OF THE VERTEBRATE BRAIN* ** *JUNE 17 ? 29, 2010* *Application deadline: April 30, 2010* Instructors: Partha Mitra, Kathy Rockland & Z. Josh Huang *Please pass this along to colleagues or members of your laboratory or group who may benefit from this training. * In comparison with complete reference genomes now available for multiple species, our knowledge about the neuronal and circuit architecture of the vertebrate nervous systems is relatively sparse. However, this situation is rapidly changing, enabled by technical advances as well as resurgent and widespread interest in the neuroscientific community in mapping out neural circuitry at unprecedented scales, ranging from the reconstruction of local micro-circuits to the mapping of brain-wide meso-circuits. This circuit architecture naturally and logically complements the molecular architecture as delineated by the mapping of brain-wide gene expression patterns. Experimental efforts are under way in multiple species, promising to advance our knowledge of the wiring logic of the vertebrate brain. This will fundamentally impact our understanding of brain function and evolution, and also play an essential role in understanding pathological changes in circuitry that underlie neurological and neuropsychiatric disorders. This two week workshop will bring together classical neuroanatomical approaches along with the new techniques that are enabling a new generation of neuroanatomical research into the circuit and molecular architecture of the vertebrate brain. The workshop will have three main components: classical, molecular and computational neuroanatomy. An experimental component of the workshop will involve injection based tract tracing in the mouse, employing classical and viral tracer substances, in wild type and transgenic mice. Lectures will cover classical (tracer injections, sectioning, histochemistry, imaging) and molecular (genetic engineering of mice as well as viral tracers, optogenetic probing of circuits) techniques. Material will be presented by simultaneous viewing of slides under light microscopy as well as digital images, including an in-depth orientation to internet resources. The computational component will involve hands on algorithmic analysis and interpretation of digital neuroanatomical data sets, from both EM and light microscopy. Species covered will include rodents, human and nonhuman primates, with special lectures on other vertebrate lineages. Speakers include: John Allman, David Amaral, Katrin Amunts, Jason Bohland, Mitya Cklovskii, Karl Deisseroth, Bruce Fischl , Mike Hawrylycz , Mark Henkelman, Harvey Karten , David Kleinfeld, Kevan Martin, Marcello Rosa, Joe Safdieh , Cliff Saper , Nenad Sestan, Karel Svoboda , Larry Swanson, Menno Witter & Hongkui Zeng Partial scholarships may be available to offset tuition, room and board costs based on stated need (apply in writing). *************************************** Cold Spring Harbor Laboratory Meetings & Courses Program Please click here for our entire course program for an up-to-the-minute and in-depth grasp of the latest techniques and concepts across a wide range of biological disciplines: For a full schedule of 2010 meetings, please click here If you no longer wish to be included in our mailings, please click here<:pakaluk at cshl.edu> From neuro.informatics.at.mbl at gmail.com Thu Apr 22 18:21:23 2010 From: neuro.informatics.at.mbl at gmail.com (Neuro Informatics) Date: Thu, 22 Apr 2010 18:21:23 -0400 Subject: [BiO BB] Neuroinformatics course at Marine Biological Laboratory, Woods Hole, MA: Application Deadline has been extended to April 26th, 2010 In-Reply-To: References: Message-ID: Neuroinformatics course at Marine Biological Laboratory, Woods Hole, MA Application Deadline has been extended to April 26th, 2010 Dates: August 14th to 29th, 2010 Web: http://www.mbl.edu/education/courses/special_topics/neufo.html The objective of this two week course is to develop an understanding of the methods of managing and analyzing data sets from neurophysiological and behavioral measurements, particularly large data volumes that require systematic statistical and computational approaches. The course includes lectures on fundamental analytical methods, established and emerging applications and focused hands-on computer-based sessions. Topics include point processes (*e.g., *spike trains), continuous processes (*e.g.*, LFP/ECoG/EEG/MEG recordings, fMRI, and behavioral recordings), and methods for analyzing neuroanatomical (*e.g., *light and electron microscopy) data. Various statistical techniques for exploratory and confirmatory analysis of the data will be treated along with underlying scientific questions and potential applications. The course also includes tutorials on computer methods and discussions of major open issues in the field. The course is targeted broadly, from experimental researchers to researchers with a theoretical or analytical orientation who work closely with data. A main aim of the course is to foster close working relations between the theorists and experimentalists. Researchers at all levels, from advanced graduate student to working professional, may benefit from the course. Limited to 26 participants. Computer Laboratory: A hands-on approach will be taken in a computer laboratory that forms an integral part of this course. Example data sets will be supplied, and participants are encouraged to bring their own data. We will primarily use MATLAB, with additional tools used as needed (*e.g.*, MySQL). Participants will be guided in applying analytical techniques to the example data sets and will further participate in a structured "data analysis challenge", in which teams will analyze published data sets in the context of specific questions. This should benefit both experimental researchers that wish to analyze their own data sets and theorists who want to work with data. Structure of the Course: The first week will contain lectures dealing with fundamental statistical and analytical techniques appropriate for neural data analysis. A concurrent computer laboratory will run in the evenings to supplement the lectures. The second week contains application-based lectures, focused on emerging research areas and associated analytical and experimental techniques, along with the "data analysis challenge". From asidhu at biomap.org Sun Apr 25 02:07:25 2010 From: asidhu at biomap.org (Amandeep Sidhu) Date: Sun, 25 Apr 2010 14:07:25 +0800 Subject: [BiO BB] CFP: 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Message-ID: IEEE CBMS 2010 23rd IEEE International Symposium on Computer-Based Medical Systems 2010 Perth, Australia, 12-15 October 2010 http://www.cbms2010.curtin.edu.au/ The 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS 2010) is intended to provide an international forum for discussing the latest results in the field of computational medicine. The scientific program of CBMS 2010 will consist of invited keynote talks given by leading scientists in the field, and regular and special track sessions that cover a broad array of issues which relate computing to medicine. RELEVANT TOPICS Network and Telemedicine Systems Medical Databases & Information Systems Computer-Aided Diagnosis Medical Devices with Embedded Computers Bioinformatics in Medicine Software Systems in Medicine Pervasive Health Systems and Services Web-based Delivery of Medical Information Medical Image Segmentation & Compression Content Analysis of Biomedical Image Data Knowledge-Based & Decision Support Systems Hand-held Computing Applications in Medicine Knowledge Discovery & Data Mining Signal and Image Processing in Medicine Multimedia Biomedical Databases CBMS 2010 invites original previously unpublished contributions that are not submitted concurrently to a journal or another conference. Many of the above listed topics are represented by corresponding Special Tracks, while others are solely covered by the general CBMS track. Prospective authors are expected to submit their contributions to one of the corresponding Special Tracks or to the general track if none of the special tracks is relevant. SPECIAL TRACKS ST1: Computational Proteomics and Genomics ST2: Knowledge Discovery and Decision Systems in Biomedicine ST3: Ontologies for Biomedical Systems ST4: HealthGrid & Cloud Computing ST5: Technology Enhanced Learning in Medical Education ST6: Intelligent Patient Management ST7: Data Streams in Healthcare ST8: Supporting Collaboration among Healthcare Workers ST9: Telemedicine ST10: Computer-Based Systems for Mental Health ST11: Image Informatics in Biomedical Research and Clinical Medicine ST12: e-Health SUBMISSION GUIDELINES Papers should be submitted electronically using EasyChair online submission system. The papers must be prepared following the IEEE two-column format and should not exceed the length of 6 (six) Letter-sized pages. LaTeX or Microsoft Word templates can be used when preparing the papers. Please, note that only PDF format of submissions is allowed. Submission web site: http://www.easychair.org/conferences/?conf=cbms2010 All submissions will be peer-reviewed by at least three reviewers. The proceedings will be published by the IEEE Computer Society Press. At least one of the authors of accepted papers is required to register and present the work at the conference; otherwise their papers will be removed from the digital library after the conference. IMPORTANT DATES Submission deadline for regular papers: 24 June 2010 Deadline for tutorial submission: 24 June 2010 Notification of acceptation for papers and tutorials: 2 Aug 2010 Final camera ready due: 2 Sep 2010 Author registration: 2 Sep 2010 INTENDED AUDIENCE Engineers, scientists, clinicians and managers involved in medical computing projects are encouraged to submit papers to the symposium and/or attend the symposium. The symposium provides its attendees with an opportunity to experience state-of-the-art research and development in a variety of topics directly and indirectly related to their own work. In addition to research papers, keynote speakers and tutorial sessions it provides participants with an opportunity to come up-to-date on important technological issues. The symposium encourages the participation of students engaged in research/development in computer-based medical systems. Organizing Committee GENERAL CHAIRS Tharam Dillon, Curtin University of Technology, Australia Daniel Rubin, National Center for Biomedical Ontologies, USA William Gallagher, University College Dublin, Ireland PROGRAM CHAIRS Amandeep Sidhu, Curtin University of Technology, Australia Alexey Tsymbal, Siemens, Germany PUBLICATION CHAIRS Mykola Pechenizkiy, Eindhoven University of Technology, Netherlands Tony Hu, Drexel University, USA SPECIAL TRACK CHAIRS Maja Hadzic, Curtin University of Technology, Australia Jake Chen, Indiana University, USA TUTORIAL CHAIRS Ya-Ping Phoebe Chen, Deakin University, Australia Xiaofang Zhou, University of Queensland, Australia PUBLICITY CHAIRS Carolyn McGregor, University of Ontario Institute of Technology, Canada Meifania Chen, Curtin University of Technology, Australia From rajkumarkannan.trichy at gmail.com Mon Apr 26 00:54:39 2010 From: rajkumarkannan.trichy at gmail.com (Kannan Rajkumar) Date: Mon, 26 Apr 2010 10:24:39 +0530 Subject: [BiO BB] Final Call for Papers: ICDEM 2010, Tiruchirappalli-India, 29-31 July 2010 Message-ID: > > *===================================* > > *Final Call for Papers with Extended Deadline* > > *====================================* > > *Due to numerous requests from authors, last date for submitting papers > ONLINE has been extended to **MAY 20, 2010* > > *=========* > > *ICDEM 2010* > > *=========* > > *ICDEM 2010 Second International Conference on Data Engineering and > Management, July 29-31 2010, Tiruchirappalli-India* > > *Organized by National Institute of Informatics-Japan and Bishop Heber > College(Autonomous)-India* > > *============* > > *PROCEEDINGS* > > *============* > > ** > > *Proceedings will be published as a **book** by a leading publisher and > selected papers by LNCS, Springer Verlag (awaiting)* > > *=======================================* > > *SPECIAL JOURNAL ISSUES FROM INDERSCIENCE* > > *=======================================* > > ** > > *Extended papers will be invited for publication in the following journals > by **Inderscience-USA** as special issues.* > > *International Journal of Intelligent Engineering Informatics (IJIEI) * > > *Special Issue on: "Data Mining Over Large Software and Courseware > Repositories"* > ** > *International Journal of Data Analysis Techniques and Strategies > (IJDATS) > **Special Issue on: "User Modelling through Real Sense Media for Adaptive > and Personalized Systems"* > > *International Journal of Multimedia Intelligence and Security (IJMIS)* > Special Issue on: "Challenges in Scalable Context Aware Multimedia > Computing" > > > *International Journal of Knowledge and Web Intelligence (IJKWI)* > > Special Issue on: "Semantic Digital Library" > ** > *=================* > > *ONLINE SUBMISSION* > > *=================* > > *Submit your papers online at * > https://cmt.research.microsoft.com/ICDEM2010/Default.aspx > > *For further details, visit conference website www.demfoundation.org* > > *=========* > > *CONTACTS* > > *=========* > > *Dr. Rajkumar Kannan (BHCT-India)* > > *Dr. Frederic Andres (CVCE-Lexembourg, NII-Japan)* > > *Program Chairs - ICDEM 2010* > > *EMAIL icdem2010 at gmail.com* > From ss2489 at cornell.edu Mon Apr 26 14:35:31 2010 From: ss2489 at cornell.edu (Surya Saha) Date: Mon, 26 Apr 2010 14:35:31 -0400 Subject: [BiO BB] Internship at Rost Lab, Munich starting in Aug, 2010 Message-ID: We are happy to announce the second internship as part of our Student Council Education and Career Central (SCCC) initiative in the Rost lab located at the Technische Universit\u00e4t M\u00fcnchen campus in Munich and starting in August, 2010. Only students from developing countries are eligible for this internship. We would also like to thank Dr. Burkhard Rost for kindly offering this internship exclusively organized by Student Council. You can find more details about the application process at http://bit.ly/iscbsccc Please contact us at internships at iscbsc.org if you have any questions. Please pass on this information to friends and colleagues in developing countries. Thanks Regards, ISCBSC Internship team From hlapp at gmx.net Mon Apr 26 19:19:04 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Mon, 26 Apr 2010 19:19:04 -0400 Subject: [BiO BB] Call for Lightning Talks open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <2AAECFD1-891C-44CE-AD27-EBA1F99A9E19@gmx.net> The Call for Lightning Talks is now open for the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/2010. See below for instructions. Lightning talks are short presentations of 5 minutes. They are ideal for drawing the attention of the audience to new developments, tools, and resources, or to subsequent events where more in-depth information can be obtained. Please also see our FAQ for more information (http://ievobio.org/faq.html#lightning ). Lightning talks will be part of the more interactive afternoon program on both conference days. Submitted talks should be in the area of informatics aimed at advancing research in phylogenetics, evolution, and biodiversity, including new tools, cyberinfrastructure development, large-scale data analysis, and visualization. Submissions consist of a title and an abstract at most 1 page long. The abstract should provide an overview of the talk's subject. Reviewers will judge whether a submission is within scope of the conference (see above). If applicable, the abstract must also state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. Review and acceptance of lightning talks will be on a rolling basis. The deadline for submission is the morning of the first day of the conference (June 29). Note that the number of lightning talk slots is finite, and given the high volume of submissions we experienced for full talks, the Lightning Talks track may fill up early. We cannot accept lightning talks until the open-source requirements are met, and so waiting with that until the deadline risks that the track is full by that time. We ask all submitters of lightning talks to be willing to also serve as reviewers of such, as described above. Lightning talks are only 1 of 5 kinds of contributed content that iEvoBio will feature. The other 4 are: 1) Full talks (closed), 2) Challenge entries, 3) Software bazaar demonstrations, and 4) Birds-of- a-Feather gatherings. The Call for Challenge entries remains open (see http://ievobio.org/challenge.html) , and information on the Software Bazaar and Birds-of-a-Feather sessions is forthcoming. More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/iEvoBio. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2010 Organizing Committee: Rod Page (University of Glasgow) Cecile Ane (University of Wisconsin at Madison) Rob Guralnick (University of Colorado at Boulder) Hilmar Lapp (NESCent) Cynthia Parr (Encyclopedia of Life) Michael Sanderson (University of Arizona) (*) iEvoBio and its sponsors are dedicated to promoting the practice and philosophy of Open Source software development (see http://www.opensource.org/docs/definition.php) and reuse within the research community. For this reason, if a submitted talk concerns a specific software system for use by the research community, that software must be licensed with a recognized Open Source License (see http://www.opensource.org/licenses/), and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs, Subversion, git, Bazaar, or Mercurial. From dan.bolser at gmail.com Tue Apr 27 03:52:01 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 27 Apr 2010 08:52:01 +0100 Subject: [BiO BB] Fwd: [Bioperl-l] Google Summer of Code - accepted students In-Reply-To: <4BD60D63.1040400@cornell.edu> References: <4BD60D63.1040400@cornell.edu> Message-ID: ---------- Forwarded message ---------- From: Robert Buels Date: 26 April 2010 23:02 Subject: [Bioperl-l] Google Summer of Code - accepted students To: rmb32 at cornell.edu Hi all, I'm pleased to announce the acceptance of OBF's 2010 Google Summer of Code students, listed in alphabetical order with their project titles and primary mentors: Mark Chapman (PM Andreas Prlic) - Improvements to BioJava including Implementation of Multiple Sequence Alignment Algorithms Jianjiong Gao (PM Peter Rose) - BioJava Packages for Identification, Classification, and Visualization of Posttranslational Modification of Proteins Kazuhiro Hayashi (PM Naohisa Goto) - Ruby 1.9.2 support of BioRuby Sara Rayburn (PM Christian Zmasek) - Implementing Speciation & Duplication Inference Algorithm for Binary and Non-binary Species Tree Joao Pedro Garcia Lopes Maia Rodrigues (PM Eric Talevich) - Extending Bio.PDB: broadening the usefulness of BioPython's Structural Biology module Jun Yin (PM Chris Fields) - BioPerl Alignment Subsystem Refactoring Congratulations to our accepted students! All told, we had 52 applications submitted for the 6 slots (5 originally assigned, plus 1 extra) allotted to us by Google. Proposals were extremely competitive: 6 out of 52 translates to an 11.5% acceptance rate. ?We received a lot of really excellent proposals, the decisions were not easy. Thanks very much to all the students who applied, we very much appreciate your hard work. Here's to a great 2010 Summer of Code, I'm sure these students will do some wonderful work. Rob Buels OBF GSoC 2010 Administrator _______________________________________________ Bioperl-l mailing list Bioperl-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioperl-l From wangk at chgc.sh.cn Tue Apr 27 00:43:37 2010 From: wangk at chgc.sh.cn (wangk at chgc.sh.cn) Date: Tue, 27 Apr 2010 12:43:37 +0800 (CST) Subject: [BiO BB] How can I obtain TRANSFAC Message-ID: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> Hi I need TRANSFAC (http://www.gene-regulation.com/pub/databases.html) to predicate TFs and their TFBSs, but confused in finding out how can I obtain the TRANSFAC dataset. Is there someone who can give me some help? Kai From mmokrejs at ribosome.natur.cuni.cz Tue Apr 27 13:37:05 2010 From: mmokrejs at ribosome.natur.cuni.cz (Martin Mokrejs) Date: Tue, 27 Apr 2010 19:37:05 +0200 Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? In-Reply-To: <6fe131b0.8534.128149cbc37.Coremail.oceanhu@126.com> References: <1271067345593.pj.siivola.44727.ckBCb86fobw0f01X_qTaxQ@luukku.com>, , <4BC867AC.1010309@gmail.com> <6fe131b0.8534.128149cbc37.Coremail.oceanhu@126.com> Message-ID: <4BD720C1.9020602@ribosome.natur.cuni.cz> Go for http://h-invitational.jp M. ocean wrote: > > > Hi Kieslowski, > > for the 3'UTR, for my experience, i think the annotation from refseq is more accurate, and so more reliable, but it might loose some 3'UTRs which are real and annotated by Ensembl but missing in refseq. For Ensembl annotation, it's true there are many more Transcripts with annotated 3'UTR comparing with refseq anntation. which database to choose, it just depends. > > best, > Huhaiyang > > CAS-MPG Partner Institute for Computational Biology (PICB) > Shanghai Institutes for Biological Sciences (SIBS) > Chinese Academy of Sciences (CAS) > 320 Yueyang Road, Shanghai 200031, P.R.China > Tel:(86)-21-54920218 > > > > ?2010-04-17?"Seema Trivedi" ??? >> >> Hello kieslowski >> >> Try biomart of Ensembl. choose the Homo sap. option and choose the Ensembl gene (anyway the default), on features choose the UTRs and then click results. If you have a limited number of gene list, you can paste it in the box just beneath the gene/transcript etc. option. If you find it difficult there are tutorial on the Ensembl website itself and possibly on the YouTubes as well. >> >> All the best >> >> Seema Trivedi >> Associate Professor >> Dept. of Zoology >> JN Vyas University >> Jodhpur (Raj) >> 342001 >> India >> >> >> >> >>> Date: Fri, 16 Apr 2010 15:35:40 +0200 >>> From: kry.kieslowski at gmail.com >>> To: bbb at bioinformatics.org >>> Subject: [BiO BB] How can I find reliable database of Human 3' UTRs ? >>> >>> Dear BBB forum members >>> >>> For my thesis, I was looking for reliable database of Human 3' UTRs. >>> Could someone please help me for that. I would really appreciate. >>> >>> Thanks From dan.bolser at gmail.com Wed Apr 28 03:00:16 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 28 Apr 2010 08:00:16 +0100 Subject: [BiO BB] How can I obtain TRANSFAC In-Reply-To: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> References: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> Message-ID: Looks like you're out of luck. From the transfac website: "We strongly support the collaborative nature of scientific research that is the basis of our products." However, words like those are cheap, but downloading transfac isn't. It'll cost you 500 euro (per year, as an academic) to download the 'database', but it isn't clear if you can easily get access to the data [1]. Perhaps there are some free alternatives or pirated copies of transfac available? Cheers, Dan. [1] http://emboss.open-bio.org/pipermail/emboss/2003-March/000993.html On 27 April 2010 05:43, wrote: > Hi > > I need TRANSFAC (http://www.gene-regulation.com/pub/databases.html) to > predicate TFs and their TFBSs, but confused in finding out how can I obtain > the TRANSFAC dataset. > > Is there someone who can give me some help? > > Kai > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From ketil.malde at imr.no Wed Apr 28 01:07:50 2010 From: ketil.malde at imr.no (Ketil Malde) Date: Wed, 28 Apr 2010 07:07:50 +0200 Subject: [BiO BB] How can I obtain TRANSFAC In-Reply-To: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> (wangk@chgc.sh.cn's message of "Tue, 27 Apr 2010 06:43:37 +0200") References: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> Message-ID: <87bpd45fmh.fsf@malde.org> "wangk at chgc.sh.cn" writes: > I need TRANSFAC (http://www.gene-regulation.com/pub/databases.html) to > predicate TFs and their TFBSs, but confused in finding out how can I obtain > the TRANSFAC dataset. I believe TRANSFAC is proprietary. An alternative might be Jaspar. >From http://jaspar.genereg.net/ The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc) consist of the open data acess, non-redundancy and quality. -k -- If I haven't seen further, it is by standing in the footprints of giants From Manjula.Thimma at KAUST.EDU.SA Wed Apr 28 02:11:50 2010 From: Manjula.Thimma at KAUST.EDU.SA (Manjula P. Thimma) Date: Wed, 28 Apr 2010 09:11:50 +0300 Subject: [BiO BB] Programmatic access to pubmed Message-ID: Dear All, I am heading to create a list of reference articles that discuss about Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or in any part of the text) from pubmed. Since Manual fishing is cumbersome, I am wondering is there any programmatic access for this database? Any pointers towards this is much appreciated. Best Regards Manjula From pmr at ebi.ac.uk Wed Apr 28 03:10:52 2010 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 28 Apr 2010 08:10:52 +0100 Subject: [BiO BB] How can I obtain TRANSFAC In-Reply-To: References: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> Message-ID: <4BD7DF7C.2070802@ebi.ac.uk> Dear Kai, On 04/28/10 08:00, Dan Bolser wrote: > Looks like you're out of luck. From the transfac website: > > "We strongly support the collaborative nature of scientific > research that is the basis of our products." > > > However, words like those are cheap, but downloading transfac isn't. > > It'll cost you 500 euro (per year, as an academic) to download the > 'database', but it isn't clear if you can easily get access to the > data [1]. > > Perhaps there are some free alternatives or pirated copies of transfac > available? In EMBOSS we switched to using JASPAR: http://jaspar.genereg.net/ Hope this helps, Peter Rice From maximilianh at gmail.com Wed Apr 28 06:01:56 2010 From: maximilianh at gmail.com (Maximilian Haussler) Date: Wed, 28 Apr 2010 11:01:56 +0100 Subject: [BiO BB] How can I obtain TRANSFAC In-Reply-To: References: <1850.58.198.96.207.1272343417.squirrel@mail.chgc.sh.cn> Message-ID: try Jaspar http://bergmanlab.smith.man.ac.uk/?p=452 or uniprobe http://the_brain.bwh.harvard.edu/uniprobe/ for free alternatives. good luck Max On Wed, Apr 28, 2010 at 8:00 AM, Dan Bolser wrote: > Looks like you're out of luck. From the transfac website: > > ? ? ? ?"We strongly support the collaborative nature of scientific > research that is the basis of our products." > > > However, words like those are cheap, but downloading transfac isn't. > > It'll cost you 500 euro (per year, as an academic) to download the > 'database', but it isn't clear if you can easily get access to the > data [1]. > > Perhaps there are some free alternatives or pirated copies of transfac > available? > > > Cheers, > Dan. > > > [1] http://emboss.open-bio.org/pipermail/emboss/2003-March/000993.html > On 27 April 2010 05:43, ? wrote: >> Hi >> >> I need TRANSFAC (http://www.gene-regulation.com/pub/databases.html) to >> predicate TFs and their TFBSs, but confused in finding out how can I obtain >> the TRANSFAC dataset. >> >> Is there someone who can give me some help? >> >> Kai >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From paolo.romano at istge.it Wed Apr 28 11:29:16 2010 From: paolo.romano at istge.it (Paolo Romano) Date: Wed, 28 Apr 2010 17:29:16 +0200 Subject: [BiO BB] Programmatic access to pubmed In-Reply-To: References: Message-ID: <201004281530.o3SFTJql015509@clus2.istge.it> Hello Manjula, you may be interested in testing PubClust at: http://biocomp.o2i.it/bioCOMP/main.php?object=application_toMine&action=view . It's a clustering system aimed at group results from pubmed by similarity of terms in abstracts and authors. You could, e.g., query for Cancer Metabolomics NMR and have results grouped by similarity of abstracts' contents. Ciao. Paolo At 08.11 28/04/2010, Manjula P. Thimma wrote: >Dear All, > >I am heading to create a list of reference articles that discuss >about Cancer Metabonomics/Metabolomics using NMR (either in the >abstract, or in any part of the text) from pubmed. Since Manual >fishing is cumbersome, I am wondering is there any programmatic >access for this database? > >Any pointers towards this is much appreciated. > >Best Regards >Manjula >_______________________________________________ >BBB mailing list >BBB at bioinformatics.org >http://www.bioinformatics.org/mailman/listinfo/bbb Paolo Romano (paolo.romano at istge.it) Bioinformatics National Cancer Research Institute (IST) From kanzure at gmail.com Wed Apr 28 11:34:20 2010 From: kanzure at gmail.com (Bryan Bishop) Date: Wed, 28 Apr 2010 10:34:20 -0500 Subject: [BiO BB] Programmatic access to pubmed In-Reply-To: References: Message-ID: On Wed, Apr 28, 2010 at 1:11 AM, Manjula P. Thimma wrote: > I am heading to create a list of reference articles that discuss about Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or in any part of the text) from pubmed. Since Manual fishing is cumbersome, I am wondering is there any programmatic access for this database? How about something like this? http://hublog.hubmed.org/archives/001518.html - Bryan http://heybryan.org/ 1 512 203 0507 From vasant.marur at gmail.com Wed Apr 28 12:15:48 2010 From: vasant.marur at gmail.com (Vasant Marur) Date: Wed, 28 Apr 2010 12:15:48 -0400 Subject: [BiO BB] Programmatic access to pubmed In-Reply-To: References: Message-ID: And here's a HOWTO:?Download a large, custom set of records from NCBI http://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/ On Wed, Apr 28, 2010 at 11:34 AM, Bryan Bishop wrote: > > On Wed, Apr 28, 2010 at 1:11 AM, Manjula P. Thimma wrote: > > I am heading to create a list of reference articles that discuss about Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or in any part of the text) from pubmed. Since Manual fishing is cumbersome, I am wondering is there any programmatic access for this database? > > How about something like this? > > http://hublog.hubmed.org/archives/001518.html > > - Bryan > http://heybryan.org/ > 1 512 203 0507 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb -- My Blog -->http://blog.vasantmarur.net Niels Bohr - "Prediction is very difficult, especially if it's about the future." From insight.robin at gmail.com Wed Apr 28 15:32:23 2010 From: insight.robin at gmail.com (Rob C) Date: Wed, 28 Apr 2010 15:32:23 -0400 Subject: [BiO BB] Programmatic access to pubmed In-Reply-To: References: Message-ID: You can create a robot to automate this. This demo http://irobotsoft.com/help/record%20robot.swf shows a simple example. Here http://irobotsoft.com/help/ has more information. On Wed, Apr 28, 2010 at 2:11 AM, Manjula P. Thimma < Manjula.Thimma at kaust.edu.sa> wrote: > Dear All, > > I am heading to create a list of reference articles that discuss about > Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or in > any part of the text) from pubmed. Since Manual fishing is cumbersome, I am > wondering is there any programmatic access for this database? > > Any pointers towards this is much appreciated. > > Best Regards > Manjula > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From genehack at genehack.org Wed Apr 28 15:45:19 2010 From: genehack at genehack.org (John SJ Anderson) Date: Wed, 28 Apr 2010 15:45:19 -0400 Subject: [BiO BB] Programmatic access to pubmed In-Reply-To: (Manjula P. Thimma's message of "Wed, 28 Apr 2010 09:11:50 +0300") References: Message-ID: <86hbmvxsxc.fsf@genehack.org> "Manjula P. Thimma" writes: > I am heading to create a list of reference articles that discuss about > Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or > in any part of the text) from pubmed. Since Manual fishing is > cumbersome, I am wondering is there any programmatic access for this > database? You mean like, ? john. -- "Faith which does not doubt is dead faith." - Miguel de Unamuno From dan.bolser at gmail.com Thu Apr 29 13:52:13 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Thu, 29 Apr 2010 18:52:13 +0100 Subject: [BiO BB] Programmatic access to pubmed In-Reply-To: References: Message-ID: There was a related discussion on the bio2RDF mailing list (below). HTH, Dan. From: Marc-Alexandre Nolin To: bio2rdf at googlegroups.com Mailing-list: list bio2rdf at googlegroups.com; contact bio2rdf+owners at googlegroups.com List-Post: , List-Help: , List-Archive: Sender: bio2rdf at googlegroups.com Hello, I've finally put online a new version of Pubmed/medline at http://pubmed.bio2rdf.org/sparql The release information and copyrights notice are available on the release endpoint http://release.bio2rdf.org/sparql or throw the Bio2RDF service with the URI http://bio2rdf.org/release:pubmed This release use nquads, so you can get the complete triples from a single document whatever its depth from the main URI by specifying its graph. For example, take a random pubmed ID, 17472304, so to get the complete information about this record, you can ask the sparql query select * where {graph {?s ?p ?o}} The RDFizer program used to create it is indicated in the release information. Comments, request for change, anythings are welcome. Thanks, Marc-Alexandre Nolin -- You received this message because you are subscribed to the Google Groups "bio2rdf" group. To post to this group, send email to bio2rdf at googlegroups.com. To unsubscribe from this group, send email to bio2rdf+unsubscribe at googlegroups.com. For more options, visit this group at http://groups.google.com/group/bio2rdf?hl=en. On 28 April 2010 07:11, Manjula P. Thimma wrote: > Dear All, > > I am heading to create a list of reference articles that discuss about Cancer Metabonomics/Metabolomics using NMR (either in the abstract, or in any part of the text) from pubmed. Since Manual fishing is cumbersome, I am wondering is there any programmatic access for this database? > > Any pointers towards this is much appreciated. > > Best Regards > Manjula > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From christoph.gille at charite.de Thu Apr 29 04:47:08 2010 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Thu, 29 Apr 2010 10:47:08 +0200 Subject: [BiO BB] Programmatic access to pubmed Message-ID: In our team we reconstruct metabolic networks and therefore we need to screen hundreds of pubmed references to find evidences for certain metabolic reactions in the literature. We use this simple Java-application: http://www.bioinformatics.org/strap/strap.php?pubmed=t We proceed as follows: We make a list of Pmid-numbers. We move the mouse over the list and then we go for a coffee to give the system sufficient time to cache the Abstracts. Then we move again the mouse over the list of PMID numbers. This time we observe color text high-lightings (defined by Ctrl-F "Find") to appear in the abstract panel. If abstract is too big, then the high-lightings may appear in the vertical scroll-bar of the text panel. The system might automatically identify full text links by following the links provided by NCBI. In all cases PDF can be manually associated. In this case this visual text-mining can be performed for full text. http://www.bioinformatics.org/strap/strap.php?pubmed=t Appart from this, professional Literature managers such as Jabref or Mendeley are able to load lists of pubmed abstracts. From christoph.gille at charite.de Fri Apr 30 09:46:01 2010 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 30 Apr 2010 15:46:01 +0200 Subject: [BiO BB] reading frame, putative protein Message-ID: <3a679ebae8d7dfb8909a367ea8db9d61.squirrel@webmail.charite.de> Perhaps you could help with a reading frame problem: I want to verify or reject the hypothesis that there is a yet unknown putative reading frame in a known coding viral gene. The translated amino acid sequence does not yield any blast or prosite hits. Question: how can I verify by computational methods, that this could be indeed an additional coding reading frame, resulting in an amino acid sequence for which no similar sequence exist in todays databases. What I would do: I would first check in related sequences that the reading frame is indeed open. Then I could look for irregularities in codon usage resulting from the two overlapping reading frames. Then I might observe absense of base wobbling in the third position due to the other reading frame. What would you suggest? What else could I do? Can you recommend any search for functional sites? All methods based on sequence similarity will fail since there is no similar sequence so far. Many thanks Christoph