From cbaker from i2r.a-star.edu.sg Thu Jul 10 09:07:50 2008 From: cbaker from i2r.a-star.edu.sg (Christopher J. O. Baker) Date: Thu Jul 10 11:53:12 2008 Subject: [Bionews] REVISED DEADLINE - ECCB 2008 Workshop: Annotation, interpretation and management of Mutations (AIMM)- call for papers References: <2dbc82b00801260159j7996fb52n663da78315d2d254@mail.gmail.com> <162B8AFBFBBB2148A9A1B8F9C57534280261960F@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B1422@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B162C@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B162F@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B1634@mailbe01.teak.local.net> <162B8AFBFBBB2148A9A1B8F9C5753428042B1635@mailbe01.teak.local.net> Message-ID: <162B8AFBFBBB2148A9A1B8F9C5753428042B1676@mailbe01.teak.local.net> Dear Researcher, Due to requests for an extension of the paper submission deadline for the AIMM2008, we decided revise it to July 18th (start of SIG meetings at the ISMB2008). Only minor extension can be granted thereafter. In addition, we encourage the submission of short position papers on topics that have not yet been published in research publications, including proposals outlining how to address the representation and integration of phenotypic information for the annotation of genotypic variability. We look forward to seeing you in Sardinia AIMM workshop @ ECCB 2008 =================================================================================================== ECCB 2008 Workshop: Annotation, interpretation and management of Mutations (AIMM) - call for papers =================================================================================================== Preamble: Genetic variability (SNPs, mutations) plays a key role in the analysis of genetic mechanisms and complex diseases. The effort in the gathering and understanding of the information regarding human variability is large, e.g. data collection from the 1000 genomes project. In step with such initiatives this workshop will focus on solutions in text mining, data warehousing and machine learning that allow better integration of mutation relevant information into a bioinformatics infrastructure. Altogether, the meeting participants will discuss the methods for the prediction of phenotypic effects induced by mutations, support to clinical decision processes involving mutations and the means that allow access and management of mutations with annotations from different data resources. Synergistic use of these technologies should facilitate inference of knowledge from sequence to structure to function and to phenotypes. The workshop brings together members of different disciplines to improve know-how and technology transfer as well as better hypothesis generation for yet un-annotated mutations. Keynote Speakers: Catherine Worth Leibniz-Institut f. Molekulare Pharmakologie, Berlin, DE In Collaboration with Tom Blundell, Cambridge, UK Kevin B. Cohen, The Hunter Lab, Center for Computational Pharmacology University of Colorado Health Sciences Center, Colorado, US Intended audience: This workshop reaches out to the following participants: data architects working on data modeling and knowledge representation, data warehouse curators seeking to address a backlog of un-curated mutations from the literature, designers of mining solutions and services for unstructured text, machine learning specialists developing classifiers for predictive analyses, structural biologists involved in protein engineering and physicians involved in genome scale population studies. The workshop includes keynote talks reporting on the management of SNP data and giving better insights on the importance of non-synonymous SNPs on diseases. Submissions: We invite both long (4000 words / 12 pages) and short papers (2000 words / 6 pages) on the topics listed below. Manuscript preparation and formatting instructions are available at the following website http://www.ebi.ac.uk/Rebholz-srv/aimm-instructions.html We encourage proposals for workshop presentations that describe: * Infrastructures and metadata to support archival and study of perturbations (mutations) and variations (SNPs) within biological systems. * Integration of mutation-related data into systems level analysis of a biological sciences (disease, biomarkers, clinical, metabolomics). * Novel techniques (information extraction, machine learning and others solutions) for the extraction of mutations and generation of annotations from the scientific literature. * Tools and analyses predicting the impacts of mutations * Hypothesis generation and reuse: building the derived insights of mutational studies into biological models Submissions can be made through the EasyChair submission page: http://www.easychair.org/conferences?conf=aimm2008 All papers will be published in an online workshop proceedings with CEUR http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/ Long papers may be invited to submit extended versions to a special issue of BMC Bioinformatics. Organizers Christopher J. O. Baker , PhD Principal Investigator Data Mining Department Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613 Tel: +65 6874 3495 Email: cbaker@i2r.a-star.edu.sg Dietrich Rebholz-Schuhmann, MD, PhD Research Group Leader European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, CB101SD, United Kingdom Tel: +44 (0)1223 492 594 Email: Rebholz@ebi.ac.uk Important Deadlines: Paper Submission: July 7th Acceptance: August 4th Final Manuscripts: August 18th Workshop: Monday, September 22, 2008 Venue: ECCB2008 @ Cagliari, Sardinia - Italy Session Topics: Mutation Databases and Metadata: Design, Content, Accuracy. =========================================================== Over 400 mutation databases can be found with a 'google' search. Many are no longer maintained and cover very specific data sets. These repositories have been designed to support a wide range of features from SNPs, point mutations, insertions, deletions, and observed phenotypes. Furthermore they incorporate a wide range of modified protein features and metrics in the accompanying annotations to the mutation descriptions. In the main these databases are manually curated however mutation annotations are frequently inaccurate e.g. in the PDB, inaccurate to the degree of 40 % of all PDB records. Extraction of mutations and annotations from literature: ======================================================== AI techniques such as text mining and natural language processing have been used to enable . A number of systems have been developed generally showing that extraction mutations from texts can be achieved with high levels of precision and recall. These systems remain prototype scale their adoption to measure the accuracy, recreation and update of existing mutation databases as we as their incorporation into semi manual annotation pipelines is the next milestone. In addition there is continuing discussion over the appropriate metrics for individual tasks within these systems which requires community involvement. This emergent technology now needs standardization. Predicting the impacts of Mutations: ==================================== The ability to predict the impact of a mutation or the consequence of a sequence variant is central to the diagnosis of genetic diseases. Non-synonymous mutations may impact translational regulation, mRNA stability, mRNA splicing and rates of translation. Proteins affected by nsSNPs may have altered; catalytic sites, stability, ability to aggregate, and or posttranslational modifications. Moving from SNP to sequence to structure and function has been addressed with varying degrees of accuracy with sequence and structure based (molecular mechanism, empirical energy function or machine learning) methods. The need to apply such techniques at a genome scale requires that robust approaches are identified, benchmarked with standard metrics in order to assign valid significance to ns mutations. Reuse of existing mutation databases for checking quality of predictions is pivotal. Mutation Data Integration and Reuse: Panel Discussion ===================================================== http://www.ebi.ac.uk/Rebholz-srv/aimm.html ********************** ANNOUNCEMENT ******************************** We are moving to Fusionopolis! With effect of Monday, 28 July 2008, our official address will be: Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, Singapore 138632. Main line: +65 64082000. Please visit http://www.fusionopolis.a-star.edu.sg/ for more information on Fusionopolis. ******************************************************************* ------------ Institute For Infocomm Research - Disclaimer -------------This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you -------------------------------------------------------- From Mike.Fursov from gmail.com Wed Jul 23 09:47:23 2008 From: Mike.Fursov from gmail.com (Mikhail Fursov) Date: Wed Jul 23 12:50:35 2008 Subject: [Bionews] UGENE v1.1 released Message-ID: <17b6ee03-7dff-4605-9c4a-8bf13502f3ca@m36g2000hse.googlegroups.com> About: UGENE is a free software aimed to integrate most of the important molecular biology tools within a single graphical environment that runs fast both on Linux and Windows systems and is able to utilize resources of modern multi-core hardware. Some of new features in version 1.1: * Graphical interface and integration of HMMER2 command line tools. * Support for gzipped data files ... The complete list of features is available here: http://ugene.unipro.ru/changelist.html Link: http://ugene.unipro.ru From rm285 from georgetown.edu Mon Jul 28 15:33:05 2008 From: rm285 from georgetown.edu (Raja Mazumder) Date: Mon Jul 28 21:01:09 2008 Subject: [Bionews] UniProt Release Note 14.0 Message-ID: <488E2D01.209@georgetown.edu> Dear UniProt Users, ******************************************************************************** UniProt Release 14 Note 22-July-2008 ******************************************************************************** CONTENTS 1. Introduction 2. Database description 3. Current release contents 4. Description of changes made to UniProt since release 13.0 5. Forthcoming changes 6. How to link to UniProt 7. Feedback 8. Acknowledgements 9. Terms of use 10. Citation 11. Contact 1. INTRODUCTION The UniProt Consortium--European Bioinformatics Institute (EBI), Swiss Institute of Bioinformatics (SIB) and Protein Information Resource (PIR)--is pleased to announce UniProt Release 14 (22-July-2008). UniProt is updated every three weeks, and can be accessed online for searches or download at http://www.uniprot.org. 2. DATABASE DESCRIPTION The Universal Protein Resource (UniProt), a collaboration between the European Bioinformatics Institute (EBI), Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB), is comprised of four databases, each optimized for different uses. The UniProt Knowledgebase (UniProtKB) is the central access point for extensively curated protein information, including function, classification and cross-references. The UniProt Reference Clusters (UniRef) combine closely related sequences into a single record to speed up sequence similarity searches. The UniProt Archive (UniParc) is a comprehensive repository of all protein sequences, consisting only of unique identifiers and sequences. The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. Additional information on UniProt is available at ftp://ftp.uniprot.org/pub/databases/uniprot/README and in the UniProt Knowledgebase user manual (http://www.uniprot.org/docs/userman.htm). 3. CURRENT RELEASE CONTENTS ------------------------------------------------------------- UniProt Release 14 ------------------------------------------------------------- Database -- Entries ------------------------------------------------------------- UniProtKB -- 6,462,752 (UniProtKB/Swiss-Prot section: 392,667; UniProtKB/TrEMBL section: 6,070,084) UniRef100 -- 6,229,158 UniRef90 -- 4,169,699 UniRef50 -- 1,987,164 UniParc -- 17,159,442 UniMES -- 6,028,191 ------------------------------------------------------------- Detailed release statistics for UniProtKB/Swiss-Prot and UniProtKB/TrEMBL sections of the UniProt Knowledgebase can be viewed at http://www.uniprot.org/docs/relnotes.htm#SPstat and http://www.uniprot.org/docs/relnotes.htm#TRstat, respectively. 4. DESCRIPTION OF CHANGES MADE TO UNIPROT SINCE RELEASE 13.0 UniProt Knowledgebase - To learn about the changes since the last major release please read the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL release notes (http://www.uniprot.org/docs/relnotes.htm) and the recent changes document (http://www.uniprot.org/docs/sp_news.htm). 5. FORTHCOMING CHANGES Forthcoming changes concerning the UniProt Knowledgebase are described in http://www.uniprot.org/docs/sp_soon.htm and http://www.uniprot.org/docs/xml_soon.htm. 6. HOW TO LINK TO UNIPROT ENTRIES How to link to UniProt entries can be found at http://www.uniprot.org/faq/28#retrieving 7. FEEDBACK We are constantly trying to improve our database in terms of accuracy and representation and hence, consider your feedback extremely valuable. Please contact us (http://www.uniprot.org/contact) if you have any questions or comments . Submit new sequence data, updates and corrections at http://www.uniprot.org/help/submissions. 8. 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