| News & Commentary |
NCBI is pleased to announce the availability of Perl and Python interfaces to the NCBI C++ Toolkit for Intel Linux platforms. These interfaces provide access to most of the Toolkit's functionality ([link]) from the Perl and Python programming languages.
AVAILABILITY:
They are available as binary releases under ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/, in the Perl and Python subdirectories. We welcome any feedback about these newly available tools.
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GenCLiP, a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords, is now published in the BMC Bioinformatics journal ([link]).
Two main characters of GenCliP are: (i) all of the associations between the analyzed human genes and the keywords outputted by GenCLiP are up-to-date; (ii) GenCLiP can construct gene co-occurrence networks among the analyzed genes based on custom keywords.
AVAILABILITY:
GenCLiP is freely available under the BSD Open Source license for download from http://www.genclip.com/
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LOCALE: Cagliari, on the Mediterranean island of Sardinia
DATE: Monday, September 22, 2008 (beginning of ECCB)
Probabilistic Methods for Dynamic System Models and Data Integration in Computational Biology
We cordially invite you to join us for a workshop on Probabilistic Modelling in Computational Biology affiliated with ECCB in Sardinia. The meeting will focus on Probabilistic Methods for Dynamic System Models and Data Integration in Computational Biology.
The extraction of an improved biological understanding from genome-scale quantitative measurements, like microarray data, has become a very active area of bioinformatics research. The integration of data necessary for the intelligent exploitation of contextual information provides a considerable challenge. As recent work demonstrates, probabilistic approaches prove to be promising, flexible tools in this endeavour.
The workshop will explore current advances and open issues in sessions presenting novel developments contributed by participants and introduced by invited talks from leading researchers in the field. We welcome submissions of extended abstracts by 17 August 2008 for short presentations of recent work in the field. Poster facilities are also provided.
IMPORTANT DATES:
Submission deadline: August 17, 2008
Early registration discount: August 24, 2008
FOR MORE INFORMATION:
Info & Contact: http://bioinf.boku.ac.at/pmcb/
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The bioinformatics group of the Pathogen Functional Genomics Resource Center at the J. Craig Venter Institute would like to announce the release of a new free software tool for protein quantitation. The APEX Quantitative Proteomics Tool is a free and open source Java application for the simultaneous quantitation of hundreds to thousands of proteins from standard LC-MS/MS proteomic data sets. The APEX technique is a modified spectral counting technique that uses a machine learning algorithm to improve protein abundance estimate accuracy. The APEX technique is described in a paper by Lu et al., Nature Biotechnology 25(1):117-124, 2007 and was developed by the Edward Marcotte lab at the University of Texas at Austin. This software tool is an implementation of the APEX method of protein quantitation according to this paper and with consultations with the UT group.
The APEX Quantitative Proteomics Tool has an intuitive user interface with an integrated help and information system and a detailed manual. A tutorial and sample data set are included to acquaint first time users with the mechanics of using the tool.
AVAILABILITY:
Please visit the APEX Tool web site for more information and download:
[link]
The tool is in use by our proteomics group at JCVI and we hope the community at large can benefit from this work. We are very eager to have feedback from the community in terms of future enhancements to the tool.
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LOCALE: Heriot-Watt University Earl Mountbatten Building, Riccarton campus in Edinburgh, UK
DATES: July 28 (Monday)- July 31 (Thursday), 2008
The workshop aims to bring together researchers working in membrane computing and related areas (such as computational biology, DNA computing, artificial life, theory of computation) in a friendly atmosphere enhancing communication and cooperation.
FOR MORE INFORMATION:
Detailed program: http://www.macs.hw.ac.uk/wmc9/
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Recently BII has introduced a 12 month weekend classroom program “Advance Program in Clinical Trial, Research & Data Management” which is about to commence from August 2008.
FOR MORE INFORMATION:
To join the Program, one can download the Application form from http://www.bii.in/biodlp. For further details about the Program contact:
Program Coordinator
Tel: 9818473366, 9810535368
0120-4320801 / 4320802
Email: info@bii.in
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Via BioinformaticsZen.com:
``When I wrote a post about my opinion of doing a career in bioinformatics I got the impression from the comments that this was something many people wanted more information about. Pedro and I had some discussion, and thought it might be interesting to create an online survey, to get current researchers? opinions of working in the field of bioinformatics. So, the below survey begins today (July 1) and is filled out by as many people as possible over the course the next month. The data is then released into the public domain at the start of next month (August 1). Anyone who is then interested can contribute back analysis of this data, so that on September 1 hopefully we can compile together lots of interesting statistics and graphs into a handy document discussing the highs and lows of career in bioinformatics.''
The survey can be found at the Bioinformatics.Org Career Center through July:
http://www.bioinformatics.org/jobs/
Full story:
[link]
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LOCALE: Lutherstadt Wittenberg, Germany
DATES: August 20-22, 2008
PRE-SYMPOSIUM MEETING:
Software Tutorial: Data Integration for Systems Biology using the ONDEX system
[link]
The poster and software submission deadline is 31st July 2008. You are invited to submit poster or software demos in the field of:
- Database integration
- Combined dry and wetlab studies
- Molecular databases / Data warehouses
- Errors and inconsistencies in biological databases
- Prediction and integration of metabolic and regulatory networks
- Genotype-phenotype linkage
- Protein-protein interactions
- Integrative microarray modeling and analyses
- Integrative approaches for drug design
- Computational infrastructure for biotechnology
- Virtual cell
- Tool integration and workflow systems
- Laboratory information management systems
- Computational systems biology
- Quality and consistency of biological ontologies
- Integrative modelling and simulation frameworks
- Integrative data and text mining approaches
- Network analysis
- Data visualisation and visual analytics
FOR MORE INFORMATION:
http://www.imbio.de/conference/
Program: [link]
Contact: lange AT ipk-gatersleben DOT de
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LOCALE: Vienna, Austria
DATES: December 4-6, 2008
CAMDA was founded to provide a forum for the critical assessment ofthe many different techniques used in microarray data mining (Nature 411, 885, Nature 424, 610). It aims to establish the state of the art in microarray data analysis, as well as highlight progress and identify directions of future efforts. In order to achieve these goals, CAMDA adopted the approach of a community-wide experiment, letting the scientific community analyse the same contest data sets.
Researchers worldwide are invited to take the CAMDA challenge. Accepted submissions will be asked to give an oral presentation. Results of analysis are discussed and compared at the CAMDA conference. As a special opportunity, this year, a selection of analysis predictions will also be verified experimentally by the laboratory collecting the original contest data set. CAMDA provides a unique environment for testing and demonstrating your latest analysis methods.
IMPORTANT DATES:
Public release of Contest Data Set: June 1, 2008
Extended Abstract Proposals due: Sept. 28, 2008
Acceptance notification for session speakers: Nov. 1, 2008
Acceptance notification for poster presenters: Nov. 1, 2008
Early registration closes: Nov. 3, 2008
Conference opens (late p.m.): Dec. 4, 2008
Conference closes: Dec. 6, 2008
Full paper submission: Jan. 31, 2009
FOR MORE INFORMATION:
Conference home http://camda.bioinfo.cipf.es/
Contest data set at [link]
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We have just released a new and substantially updated version of the MiMI Plugin for Cytoscape that gives you access to a large integrated resource of molecular interaction data, literature links and annotation. The plugin can also be loaded directly in Cytoscape (v2.6 or later) using the plugin manager.
Important new feature is support for community annotation of molecular interaction networks. See something wrong (e.g. an interaction from a yeast two hybrid experiment that you believe is not biologically significant because the two molecule are in different compartments) then you can add your own annotation flagging this interaction and share it with other users.
FOR MORE INFORMATION:
Check it out at [link]
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| Acknowledgments |
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We wish to thank the following for their support:
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