From hseker at dmu.ac.uk Thu Feb 7 16:33:59 2013 From: hseker at dmu.ac.uk (Dr. Huseyin Seker) Date: Thu, 7 Feb 2013 21:33:59 +0000 Subject: [BiO BB] Invitation as a speaker for the conference In-Reply-To: <1F2CE60B8951C941A3F9AD79D325E51E086DAF89@PJWXMB-0001L.LEC-ADMIN.dmu.ac.uk> References: <1F2CE60B8951C941A3F9AD79D325E51E086D9AC6@PJWXMB-0001L.LEC-ADMIN.dmu.ac.uk>, <1F2CE60B8951C941A3F9AD79D325E51E086DAF89@PJWXMB-0001L.LEC-ADMIN.dmu.ac.uk> Message-ID: <1F2CE60B8951C941A3F9AD79D325E51E086DB40B@PJWXMB-0001L.LEC-ADMIN.dmu.ac.uk> Dear Colleague, I am very pleased to invite you to attend and contribute to The International Conference on Applied Informatics for Health and Life Sciences (Istanbul, Turkey, 9-11 September 2013). This is a unique event where health and life sciences are meeting informatics methods and tools to address to the problems and challenges that we face in the digital age and taking place where two continents (Europe and Asia) meet. You can find details of the conference at http://genetikinfo.com/. I will be very grateful if you could please pass the conference details to your students and colleagues who may also be interested in joining us. Looking forward to meeting you in Istanbul in September 2013 Regards Huseyin Seker (Conference Chair) On behalf of the organisation committee ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr Huseyin Seker Bio-Health Informatics Research Group Centre for Computational Intelligence Faculty of Technology De Montfort University Leicester LE1 9BH United Kingdom E-mail: hseker at dmu.ac.uk Visit Us at http://www.cse.dmu.ac.uk/~hseker/BHG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jaume.bacardit at nottingham.ac.uk Fri Feb 8 12:07:20 2013 From: jaume.bacardit at nottingham.ac.uk (Jaume Bacardit) Date: Fri, 08 Feb 2013 17:07:20 +0000 Subject: [BiO BB] PhD Studentship in Biodata Mining; University of Nottingham and Crops for the Future Research Centre Message-ID: <511530C8.5030801@nottingham.ac.uk> [Apologies if you receive multiple times this announcement] --------------------------------------------------------------------- * Title: Mining the gene networks involved in water-stress response in bambara groundnut: a machine learning approach to translating traits in model species to minor crops * Location: UK and Malaysia campuses of the University of Nottingham * Open to: any applicant with suitable qualifications. No nationality restrictions * Deadline for application: As soon as a suitable candidate is identified. --------------------------------------------------------------------- Project description: Underutilised species have the potential to help diversify agriculture and to make food production more robust in the face of future challenges. The ability to use information obtained in one species to guide evaluation of another species is the underlying principle behind the use of model systems. The translation of data from models and major crop species to underutilised species is essential if underutilised species are to make a major contribution to Global Food Security or other end-uses. The ability to identify key components of trait networks relies on developing methods to search very large datasets, guided by knowledge from other systems. Machine learning techniques have been shown to be very competent at this task, as they are able to explore vast datasets to identify key genes and their interactions. Moreover, they can easily integrate multiple sources of knowledge and automatically identify the relevant parts of the system being analysed. This project will focus on the use of machine learning and bioinformatics techniques to study the process of water-related stress in bambara groundnut (an African legume) by contrasting datasets from this species with the known networks of model organisms. This legume grows successfully with varying access to water, cropping from the Namib desert in Africa to the humid tropics in Indonesia. Applicants should have a 2.1 or 1 class honours degree, or a combination of qualifications and/or experience equivalent to that level and have training in data mining techniques or bioinformatics. Previous biology experience will be an advantage for Computer Science applicants. The successful candidate should be confident working within and across a range of activities, have excellent organisational abilities, be enthusiastic and have good interpersonal skills. The student will spend time at the UK and Malaysia campuses of the University of Nottingham. At UK the student will be based at the Interdisciplinary Computing and Complex Systems (ICOS) research group (http://icos.cs.nott.ac.uk) at the School of Computer Science. In Malaysia, the student will be co-hosted by Biosciences at UNMC (www.nottingham.edu.my/biosciences/index.aspx) and the new Crops for the Future Research Centre currently under construction. The student will be registered formally at The University of Nottingham Malaysia Campus. The studentship provides full tuition fees and a monthly stipend of 4400MYR (Malaysian Rynggit), for a duration of 3 years. This studentship will remain open until a suitable candidate is found, thus we recommend applying early. Supervisor names and contact details : Festo Massawe, School of Biosciences, UNMC (festo.massawe at nottingham.edu.my) Jaume Bacardit, School of Computer Science, UoN (jaume.bacardit at nottingham.ac.uk) Sean Mayes, Plant and Crop Sciences, UoN (sean.mayes at nottingham.ac.uk)) Michael Holdsworth, Plant and Crop Sciences, UoN (michael.holdsworth at nottingham.ac.uk) ) For informal enquiries about this studentship please contact jaume.bacardit at nottingham.ac.uk - Web: http://www.cs.nott.ac.uk/~jqb/ Please quote I.D. code Bam1-004 on all correspondence. ------------------- -- ------------------------------------------------------------------- Jaume Bacardit, PhD Lecturer in Bioinformatics University of Nottingham Interdisciplinary Computing and Complex Systems Research Group, School of Computer Science, Jubilee Campus, Nottingham, NG8 1BB, UK URL: http://icos.cs.nott.ac.uk Twitter: @ICO2S Tel: +441158467044 Fax: +441159516292 Email: jaume _dot_ bacardit _at_ nottingham _dot_ ac _dot_ uk Web: http://www.cs.nott.ac.uk/~jqb Twitter: @jaumebp -------------------------------------------------------------------- This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. From admase at decsai.ugr.es Mon Feb 11 10:43:13 2013 From: admase at decsai.ugr.es (Antonio D. Masegosa) Date: Mon, 11 Feb 2013 16:43:13 +0100 Subject: [BiO BB] CFP: Workshop on Nature Inspired Cooperative Strategies for Optimization (NICSO 2013) Message-ID: <51191191.9010108@decsai.ugr.es> ******** PLEASE APOLOGIZE FOR MULTIPLE COPIES ******** *********************************************************** The VI International Workshop on Nature Inspired Cooperative Strategies for Optimization - NICSO 2013 September 2nd - 4th, 2013 Canterbury, United Kingdom http://www.nicso2013.org *********************************************************** CALL FOR PAPERS * * * IMPORTANT DATES * * * Full paper submission: April 15, 2013 Acceptance notification: May 15, 2013 Final camera ready: June 5, 2013 NICSO: September 2-4, 2013 NICSO 2013 will be the sixth edition of the International Workshop on Nature Inspired Cooperative Strategies for Optimization. This workshop aims at bringing together international researchers and practitioners from different disciplines in order to discuss recent advances and exchange ideas on the current state of the art of cooperative problem solving strategies. All submitted papers will be blind reviewed by at least two reviewers from the Program Committee. Selection criteria will be based on relevance, originality, significance, impact, technical soundness and quality of the presentation. Contributions are expected to provide original results, insights and experimental innovations. Manuscripts must be in PDF, not exceeding 12 pages and conforming to the Latex template at Instructions for Authors page for the book series Studies in Computational Intelligence (http://www.springer.com/series/7092). Contributions are welcome to submission through the system available at http://www.easychair.org/conferences/?conf=nicso2013 The accepted papers will be published in the book series on STUDIES IN COMPUTATIONAL INTELLIGENCE (Springer) (http://www.springer.com/series/7092) indexed by ISI Web of Science Conference Proceedings, DBLP, Ulrichs, SCOPUS, MathSciNet, Current Mathematical Publications, Mathematical Reviews, Zentralblatt Math: MetaPress and Springerlink. The authors of a selection of the best accepted papers will be invited to revise and extend their contributions for publication in a special issue in the JOURNAL OF MEMETIC COMPUTING (Springer) (http://www.springer.com/engineering/computational+intelligence+and+complexity/journal/12293). Target topics (but not limited to): Adaptive Behaviour Ants Colonies Amorphous Computing Artificial Life Artificial Immune Systems Bioinformatics Bio-inspired architecture Complex Systems Distributed Computing Evolutionary Algorithms Evolutionary Robotics Evolvable Systems Games and Game Theory Genetic Algorithms Genetic Programming Hyperheuristics Membrane Computing Memetic Algorithms Quantum Computing Software Self-Assembly Systems Biology Systems Coevolution Swarm Intelligence * Workshop Organizers * Fernando Esteban Barril Otero German Terrazas Antonio D. Masegosa * Steering Committee * Natalio Krasnogor David A. Pelta * Programme Committee * Alex Freitas, University of Kent, UK Andr?s R. Masegosa, University of Granada, Spain Bel?n Melian, University of La Laguna, Spain Blas J. Galv?n, University of Las Palmas de Gran Canaria, Spain Carlos Cruz Corona, University of Granada, Spain Carlos Garc?a Mart?nez, Univeristy of C?rdoba, Spain Cecilio Angulo, Technical University of Catalunya, Spain Christof Teuscher, Portland State University, US Colin Johnson, University of Kent, UK Davide Anguita, University of Genova, Italy Enrique Onieva, University of Deusto, Spain Evelyne Lutton, INRIA, France Francisco Herrera, University of Granada, Spain Gabriela Ochoa, University of Stirling, UK Gianluigi Folino, Istituto di Calcolo e Reti ad Alte Prestazioni, Italy Gisele Pappa, Universidade Federal de Minas Gerais, Brazil Giuseppe Scollo, University of Catania, Italy J. Marcos Moreno, University of La Laguna, Spain Jaume Bacardit, University of Nottingham, UK Jean-Louis Giavitto, Universit? d'Evry, France Jim Smith, University of the West of England, UK Jon Timmis, University of York, UK Jorge Casillas, University of Granada, Spain Jos? A. Moreno, University of La Laguna, Spain Jos? Alejandro Castillo, Instituto Nacional de Investigaciones Nucleares, Mexico Jos? Luis Verdegay, University of Granada, Spain Jos? Manuel Cadenas, University of Murcia, Spain Juan Jos? Merelo, University of Granada, Spain Marco Dorigo, Universit? Libre de Bruxelles, Belgium Mar?a Teresa Lamata, University of Granada, Spain Marian Gheorghe, University of Sheffield, UK Mario Pavone, University of Catania, Italy Oliver Korb, Cambridge Crystallographic Data Centre, UK Paolo Arena, University of Catania, Italy Ren? Doursat, Complex Systems Institute, France Roberto Battiti, University of Trento, Italy Shengxiang Yang , University of Leicester, UK Stefano Pizzuti, Energy, New Technologies & Envir. Agency, Italy Steven Gustafson, General Electric Global Research Center, US Thomas Stibor, GSI Helmholtz Centre for Heavy Ion Research, Germany Vincenzo Cutello, University of Catania, Italy Vincenzo Manca, University of Verona, Italy Vitorino Ramos, Technical University of Lisbon, Portugal Vittorio Maniezzo, University of Bologna, Italy Xiao-Zhi Gao, Helsinki University of Technology, Finland Kwang-Hyun Cho, Korea Advanced Institute of Science and Technology (KAIST), korea From saidi34 at hushmail.com Tue Feb 12 12:43:00 2013 From: saidi34 at hushmail.com (saidi34 at hushmail.com) Date: Tue, 12 Feb 2013 12:43:00 -0500 Subject: [BiO BB] =?utf-8?q?A_Ph=2ED=2E_Student=E2=80=99s_CRY_for_Help?= Message-ID: <20130212174300.3C938E6726@smtp.hushmail.com> A Ph.D. Student?s CRY for Help To: Prof. Hamid Arabnia, WORLDCOMP Coordinator, Professor of Computer Science, University of Georgia, USA Prof. Hamid Arabnia, I am a student from Africa and I am in the final stages of my Ph.D. work. I have a journal paper in ACM and a conference paper in WORLDCOMP. As per my university policy, I am required to have at least two research papers in peer-reviewed (refereed) international conferences or journals before I submit my synopsis/dissertation. While everything was fine, recently, WORLDCOMP was declared as a bogus conference with evidences and endorsements from scientists: https://sites.google.com/site/worlddump1 Also see http://worldcomp-fake-bogus.blogspot.com Now, my university officials have stopped me from submitting the dissertation stating that WORLDCOMP is not peer-reviewed due to the evidences in these websites. They said that WORLDCOMP is completely fake and that?s why you have not responded to the open challenge at https://sites.google.com/site/dumpconf or https://sites.google.com/site/moneycomp1 I sent many emails to you requesting to respond to the open challenge and prove that WORLDCOMP is not fake so that I can show your response to my university officials and convince them and submit my dissertation. I also asked you to email me the reviews for my paper (I never received them, although your acceptance email stated that the paper was reviewed by two experts) but you are not responding. Recall that when I met you in WORLDCOMP, you offered me a reference letter and invited me to organize a session in the next conference and promised free registration for my next paper if I get at least five registered papers fr om others. Now I am shocked with your silence. I am clueless on what to do as I will forfeit my student status unless I submit the dissertation soon. I am facing humiliation here. I was attracted by the keynote speakers, sponsors, tutorials, and University of Georgia name at WORLDCOMP website. Now I feel that I made a very critical mistake by submitting to WORLDCOMP. As the last resort, I am posting to this mailing list/forum (where WORLDCOMP details were published in the past I think) so that you understand the seriousness. I once again ask you to provide a detailed response at WORLDCOMP?s website and prove that it is not a fake (and also email me my paper reviews). I request you to focus on this issue than organizing the next conference (and create more victims like me). I hope you still have moral values. My elderly parents are dependent on me and I am crying for help. I openly beg your response! Respectfully, Saidi (this is my nickname and I am using it to avoid further humiliation. I know that you will easily identify me from this nickname and from my background mentioned above). To the forum/list owner: please understand my situation and publish this message and it will help other researchers to be more careful while choosing a conference. To the members: please help me getting a response from Prof. Arabnia. From jprudhomme at healthtech.com Wed Feb 13 11:54:44 2013 From: jprudhomme at healthtech.com (James Prudhomme) Date: Wed, 13 Feb 2013 11:54:44 -0500 Subject: [BiO BB] Conference on Structure-Based Drug Design: Genome to Drug Lead with Big Data Approach Message-ID: <009201ce0a0a$d2f93060$78eb9120$@com> ******** PLEASE FORWARD TO YOUR COLLEAGUES******** ************************************************************************** CHI/Bio-IT World's 13th Annual Structure-Based Drug Design: Genome to Drug Lead with Big Data June 19-21, 2013 Boston, MA http://www.healthtech.com/sbd ************************************************************************** At CHI/Bio-IT World's thirteenth annual Structure-Based Drug Design conference, you will hear about developments in insilico technology, as well as experimental approaches useful for accurately predicting and modeling the structures of proteins in structure-based drug design efforts. In addition, examples of successful applications of such technology approaches to genome-to-drug lead investigations will be addressed. Keynote Presentation: Drugging the Undruggable: Transforming Nature's ?-Helix into Breakthrough Medicines Tomi Sawyer, Ph.D., CSO, Aileron Therapeutics Sessions: * Structure-Based Drug Design for Kinase * Drug Resistance * Force Field Calculation * GPCR * Water & Solvation in Drug Design * Fragment-Based Drug Design * Protein-Protein Interaction * Epigenetic Targeting Scientific Advisory Board: Dr. Don Jacobs, University of North Carolina Charlotte Dr. Jon Mason, Heptares Therapeutics Ltd. Dr. Stephan Schurer, University of Miami Dr. Xiayang Qiu, Pfizer, Inc. Dr. David Dalgarno, ARIAD Pharmaceuticals, Inc. Dr. Gergely Toth, University of Cambridge Dr. Scot Mente, Pfizer Global R&D Groton Labs CALL FOR POSTERS: CHI invites researchers to present a poster to expose their research to its delegates. Accepted posters will be included in the conference proceedings. http://www.healthtech.com/Conferences_Overview.aspx?id=88586 DOWNLOAD PDF BROCHURE: http://www.healthtech.com/Conferences_Content.aspx?ekfrm=122075 HOW TO REGISTER: Web: https://chidb.com/register/2013/sbd/reg.asp Call: 781-972-5400 Email: reg at healthtech.com From zola at icis.pcz.pl Wed Feb 20 10:42:47 2013 From: zola at icis.pcz.pl (Jaroslaw Zola) Date: Wed, 20 Feb 2013 16:42:47 +0100 (CET) Subject: [BiO BB] [CfP] 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) Message-ID: <20130220154247.D76D05CAB8@icis.pcz.pl> 3rd IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) June 12-14, New Orleans, LA, USA Advances in high-throughput technologies such as DNA sequencing and mass spectrometry are profoundly transforming life sciences, resulting in the collection of unprecedented amounts of biological and medical data. Using this data to advance our knowledge about fundamental biological processes and improve human health requires novel computational models and advanced analysis algorithms. IEEE ICCABS aims to bring together leading academic and industry researchers to discuss the latest advances in computational methods for bio and medical sciences. Topics of interest include but are not limited to: * Biological modeling and simulation * Biomedical image processing * Biomedical data and literature mining * Computational genetic epidemiology * Computational metabolomics * Computational proteomics * Databases and ontologies * Gene regulation * Genome analysis * Health Informatics * High-performance bio-computing * Immunoinformatics * Molecular evolution * Population genomics * Sequence analysis * Structural bioinformatics * Systems biology * Transcriptomics Submission Instructions: Authors are invited to electronically submit extended abstracts in PDF format by following the instructions at http://www.easychair.org/conferences/?conf=iccabs13. Submissions should be prepared using IEEE Computer Society's Word/LaTeX templates available at http://www2.computer.org/portal/web/cscps/formatting and should not exceed 6 pages in length. Accepted abstracts will be published in the IEEE Xplore Digital Library. Special issues of journals on selected extended abstracts are under negotiation. A limited number of student travel awards will be made (conditional upon NSF support). Key Dates: Papers Submission: April 5, 2013 Notification of Acceptance: May 20, 2013 Author Registration: May 20, 2013 Camera-ready Papers Due: May 27, 2013 General Chairs: Srinivas Aluru (Iowa State University) Sanguthevar Rajasekaran (University of Connecticut) Program Chairs: Vladimir Filkov (UC Davis) Knut Reinert (Freie Universitat Berlin) More information at: http://www.iccabs.org/ From isbra2013 at GMAIL.COM Mon Feb 25 10:58:21 2013 From: isbra2013 at GMAIL.COM (ISBRA PC Chairs) Date: Mon, 25 Feb 2013 10:58:21 -0500 Subject: [BiO BB] Call for Abstracts: Deadline April 1 Message-ID: Dear colleague, ISBRA 2013 is now seeking submissions for Short Abstracts, with a deadline of April 1. The conference provides a pathway to publication of a manuscript for research submitted in the short abstract form. Accepted short abstracts will be distributed electronically, and selected for either oral or poster presentation at the symposium. The authors of selected short abstracts will be invited to submit full versions to a peer-reviewed supplement to be published after the symposium by BMC Bioinformatics. Submissions may be made through the EasyChair system at http://www.easychair.org/conferences/?conf=isbra2013. Instructions and format for preparation of short abstracts are available at that site. Online registration for the conference is now available at http://isbra2013.uncc.edu. We look forward to seeing you at ISBRA 2013! Cynthia Gibas, General Chair Department of Bioinformatics and Genomics University of North Carolina at Charlotte * * *Call for Papers*** *9th International Symposium on Bioinformatics Research and Applications* May 20-22, 2013, Charlotte, NC http://isbra2013.uncc.edu The *International Symposium on Bioinformatics Research and Applications* (ISBRA) provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Submissions presenting original research are solicited in all areas of bioinformatics and computational biology, including the development of experimental or commercial systems. Topics of interest include but are not limited to: Biomedical databases and data integration High-performance bio-computing Biomolecular imaging High-throughput sequencing data analysis Bio-ontologies Molecular evolution Comparative genomics and phylogenomics Molecular modeling and simulation Computational genetic epidemiology Pattern discovery and classification Computational proteomics Population genetics Data mining and visualization Software tools and applications Gene expression analysis Structural biology Genome analysis Systems biology We seek two categories of submissions: *extended abstracts* of up to 12 pages in Springer LNCS format, and *short abstracts* of up to 4 pages. Both types of submissions must be made electronically by following the instructions at http://www.easychair.org/conferences/?conf=isbra2013. Submission implies willingness of at least one author to register and present at the symposium. Accepted extended abstracts will be published prior to the symposium in Springer-Verlag's Lecture Notes in Bioinformatics (LNBI) series and presented orally at the symposium. Full versions of selected extended abstracts presented at the symposium will be invited to a peer-reviewed special issue of *IEEE/ACM Transactions on Computational Biology and Bioinformatics* *.* Accepted short abstracts will be distributed electronically and selected for either oral or poster presentation at the symposium. The authors of selected short abstracts will be invited to submit full versions to a peer-reviewed supplement to be published after the symposium by BMC Bioinformatics . Per current BMC policies, full versions of extended abstracts published in LNBI are *not* eligible for publication in the BMC supplement. *KEY DATES* *Extended Abstracts (12 pages)* *Short Abstracts (4 pages)*** *Submission deadline* * February 6, 2013* *April 1, 2013* *Notification of acceptance* *February 27, 2013* * April 15, 2013* *Final version due* * March 8, 2013* * April 22, 2013* *Steering Committee** *** *General Chair* *Program Chairs* *Dan Gusfield *(UC Davis) *Ion Mandoiu* (UConn) *Yi Pan* (GSU), Chair *Marie-France Sagot* (INRIA) *Alexander Zelikovsky (*GSU) *Cynthia Gibas *(UNCC) *Finance Chair* *Larry Mays* (UNCC) *Local Arrangements Chair* *Zhengchang Su* (UNCC)** *Zhipeng Cai *(GSU) *Oliver Eulenstein* (Iowa) *Daniel Janies* (UNCC) *Daniel Schwartz *(UConn) If you wish to unsubscribe from these messages, it is easy to do. Simply send a message to the e-mail address LISTSERV at LISTSERV.UNCC.EDU with the words SIGNOFF ISBRA2013 in the message body, and you will be automatically unsubscribed from further mailings about this year's conference. From R.Beynon at liverpool.ac.uk Tue Feb 26 03:37:27 2013 From: R.Beynon at liverpool.ac.uk (Beynon, Rob) Date: Tue, 26 Feb 2013 08:37:27 +0000 Subject: [BiO BB] A new Open Source project, Kickstarter campaign Message-ID: <6706B7CAB3880F40A7B226F437512F9253F9148D@BHEXMBX1.livad.liv.ac.uk> I would like to bring this to your attention (apologies if it has already been done). Livecode (previously incarnated as Hypercard, or Metacard or Revolution) is undergoing a radical change ? a move to make the platform Open Source. I have used this environment for amateur hacking tasks for many years, and believe that it has much more potential than I could ever realise. It is a platform for deployment across all systems (linux, mac, Windows, mobile) and is highly object oriented and starts from a GUI design. The originators of LiveCode (based in Edinburgh) are running a KickStarter campaign to make their platform open source. If you are interested in software development, in education or in open source GUI wrappers, LiveCode may be of interest. Hence, I am bringing this to your attention. The campaign has 2 days to run, and is about 15% short of target. Have a look, and if you see the potential for an open source variant, please consider support. I should also make clear I have no affiliation with LiveCode, nor do I stand to gain in any way from this posting. I hope it is within the spirit of the open source movement to bring this to your attention. http://www.kickstarter.com/projects/1755283828/open-source-edition-of-livecode Prof R J Beynon | Royal Society Industrial Fellow | Protein Function Group Institute of Integrative Biology University of Liverpool Crown Street | Liverpool | L69 7ZB +44 151 794 4312 r.beynon at liv.ac.uk http://www.liv.ac.uk/pfg