From hlapp at gmx.net Tue Feb 1 22:29:00 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Tue, 1 Feb 2011 22:29:00 -0500 Subject: [BiO BB] Registration Open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: Registration is now open for the conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/register.html . iEvoBio aims to be a forum bringing together biologists working in evolution, systematics, and biodiversity, with software developers and mathematicians. The goal of iEvoBio is both to catalyse the development of new tools, and to increase awareness of the possibilities offered by existing technologies (ranging from standards and reusable toolkits to mega-scale data analysis to rich visualization). The inaugural meeting in 2010 (see http://ievobio.org/2010) attracted over 300 participants. The 2-day meeting will take place June 21-22, 2011, in Norman, OK, jointly with the 2011 Evolution Meetings as a satellite conference. The event will feature traditional elements, including a keynote presentation at the beginning of each day and contributed talks, as well as more dynamic and interactive elements, including a challenge, lightning talk-style sessions, a software bazaar, and Birds-of-a- Feather gatherings. The topic of this year's challenge is Data Integration. Cash prizes will be awarded for first place ($1,000) and runner-up entries. The winning entries will be selected by a vote of the iEvoBio meeting participants. More details about the challenge will be provided in a separate announcement. Attendees can register jointly for Evolution and iEvoBio at a discount, or only for the iEvoBio conference. For more information about registration, venue, travel, or accommodations please visit the Evolution 2011 website at http://www.evolution2011.ou.edu/. 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 , or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Evolution (SSE) and the Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-Chair) Cynthia Parr (Encyclopedia of Life) (Co-Chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) From hlapp at gmx.net Sat Feb 5 18:43:56 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 5 Feb 2011 18:43:56 -0500 Subject: [BiO BB] Other: NESCent Seeks Hackathon Whitepapers In-Reply-To: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> References: <0D7D89E4-C0D4-4347-A94C-21800E927746@ad.unc.edu> Message-ID: The National Evolutionary Synthesis Center (NESCent), in keeping with its objective to promote collaborative development of open-source, reusable, and standards-supporting informatics resources, sponsors highly collaborative, face-to-face software development events, called "hackathons" (see [1]). To ensure that this program continues to be responsive to user needs and to tap into the expertise and creativity of the evolutionary biology community, NESCent is soliciting short whitepapers (2-6 pages) [2] on potential target areas for future hackathons. To further encourage submissions, we have now distilled specific guidelines for proposing hackathon events, based on the experiences gained from events we have sponsored in the past: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines The Center's Call for Informatics Whitepapers [3] includes not only hackathons, but also a large spectrum of other initiatives to be undertaken by the Center, including training, software development, collaborative ontology development, and coordination of data standards. Whitepapers are accepted at any time and reviewed on an on- going basis. URLs: [1] Collaborative cyberinfrastructure events and programs organized by NESCent: http://informatics.nescent.org/wiki/Main_Page [2] NESCent Call for Informatics Whitepapers http://www.nescent.org/informatics/whitepapers.php [3] Hackathon Whitepaper Guidelines: http://informatics.nescent.org/wiki/Hackathon_Whitepaper_Guidelines [4] Past NESCent-sponsored hackathons: http://informatics.nescent.org/wiki/Main_Page#Hackathons From clementsgalaxy at gmail.com Tue Feb 1 01:04:06 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Mon, 31 Jan 2011 22:04:06 -0800 Subject: [BiO BB] March 2011 GMOD Meeting: Registration is open In-Reply-To: References: Message-ID: Hello all, Registration is now open for the March 2011 GMOD Meeting ( http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting). This meeting is part of GMOD Americas 2011, an event that includes a day of Satellite Meetings, a GMOD Course (ialready full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing 192 lines. See http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda for more. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now ( http://gmod.oicr.on.ca/wiki/March_2011_GMOD_Meeting#Agenda_Proposals). For examples of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting (http://gmod.oicr.on.ca/wiki/September_2010_GMOD_Meeting), or any previous meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. Registration for the March 2011 GMOD Meeting is $80 on or before February 18 <<<<======= $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to sign up for (or propose) a Satellite Meeting (more details to come). Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Dave Clements Galaxy Project -- http://gmod.org/wiki/GMOD_Americas_2011 http://nescent.org http://usegalaxy.org/ http://getgalaxy.org From clementsgalaxy at gmail.com Thu Feb 3 20:25:48 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Thu, 3 Feb 2011 17:25:48 -0800 Subject: [BiO BB] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands In-Reply-To: References: Message-ID: We are pleased to announce the *2011 Galaxy Community Conference*, being held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. See http://galaxy.psu.edu/gcc2011/ for complete details. *About Galaxy: *Galaxy is an open, web-based platform for *accessible, reproducible, and transparent* computational biomedical research. - *Accessibility:* Galaxy enables users without programming experience to easily specify parameters and run tools and workflows. - *Reproducibility:* Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis. - *Transparency:* Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The public Galaxy service ( http://usegalaxy.org) makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs. *Conference Overview: * This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: * Talks submitted by the Galaxy community * Integration of tools (including NGS analysis tools) and distributed job management * Deployment of Galaxy instances on local resources and on the Cloud * Management of large datasets with the Galaxy Library System * Using the Galaxy LIMS functionality at NGS sequencing facilities * Visualizing Data without leaving Galaxy * Performing reproducible research * Performing and sharing complex analyses with Workflows * An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers. *Registration: * The conference fee is ?100 on or before April 24, and ?120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. See http://galaxy.psu.edu/gcc2011/Register.html * Abstract Submission: * Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html * * *Sponsors * The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a collaborative institute of the bioinformatics groups in the Netherlands. Together, these groups perform cutting-edge research, develop novel tools and support platforms, create an e-science infrastructure and educate the next generations of bioinformaticians. We are looking forward to a great conference and hope to see you in the Netherlands! The Galaxy and NBIC Teams -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From school at lipari.cs.unict.it Sat Feb 5 11:24:30 2011 From: school at lipari.cs.unict.it (Alfredo Ferro) Date: Sat, 05 Feb 2011 17:24:30 +0100 Subject: [BiO BB] Lipari CompBio 2011 -- REGISTRATION OPEN Message-ID: <201102051624.p15GOUAE007602@lipari.cs.unict.it> Biological Sequence Analysis and High Throughput Technologies REGISTRATION OPEN http://lipari.dmi.unict.it/LipariSchool/Bio/index.php Lipari, Italy, July 2 - July 9, 2011 Application deadline: May 01, 2011 Aim and scope: The dramatic rising of data being generated by high-throughput technologies, such as microarrays, ChIP-chip, ChIP-Seq data are opening a new universe of problems that will certainly provide great challenges in the coming years. The theme of the School: Biological Sequence Analysis and High Throughput Technologies will describe and highlight a few of techniques and methods for the data analysis in the era of the Personalized Genomics. The main lectures will focus on the following key topics: methods for high-throughput and parallel sequencing, data Integration and knowledge inference from high-throughput Genomic Experiments. Three special lectures will survey applications in the field of human diseases and cellular development. A series of tutorial will be also given, with the intent to complement the main lectures. These will provide snapshots of other areas that are perceived of relevance to the theme of the School. They range from introductory topics to sequence analysis to structural biology. As it is clear from the enclosed abstracts and bibliography, the selected themes have received much attention in the scholarly literature that ranges from Science, Nature, to BMC Bioinformatics, NAR and Bioinformatics. As a whole, the planned summer school will allow young researchers interested in bioinformatics and biomedicine to be exposed to cutting edge results in an area that is among the most exciting in Post-Genomic Biology. *Courses (three hours each) * Soren Brunak Data Integration In the Era of Personalized Genomics Center for Biological Sequence Analysis; Technical University of Danmark * Roderic Guigo Transcriptome Genetics Using Massively Parallel Sequencing Center de Regulalcio Genomica and Universitat Pompeu Fabra, Barcelona * Bud Mishra Genomics Redux: Man, Woman, Birth, Death, Infinity, Plus Altruism, Cheap Talks, Bad Behavior, Money, God and Diversity on Steroids New York University * Gene Myers Building Atlases Using Genetics and Light Microscopy Janelia Farm Research Campus; Howard Hughes Medical Institute * Itzik Peer High Throughput Sequencing for Comprehensively Cataloging Variants Columbia University in the City of New York * Paola Sebastiani Bayesian Networks for Analysis of High Throughput Genomic Experiments Boston University Guest lectures * Carlo Croce Causes and Consequences of miRNA Disregulation in Cancer Human Cancer Genetics Program; Ohio State University * Charles Lawrence A New Gibbs Sampler for Predicting RNA Secondary Structure for Unaligned Sequences Brown University, Providence, USA * Roded Sharan A systems-level analysis of protein networks for disease elucidation Tel Aviv University Tutorials * Matteo Comin Phylogenetic methods for biological sequences University of Padova, Italy * Peter Minary Introduction to Modern Algorithms for Conformational Sampling and Optimization in Computational Structural Biology Stanford University * Michael Levitt Computational structural biology: birth and future Stanford University * Giosu? Lo Bosco Computational models for nucleosome positions identification University of Palermo, Italy Participants will be arranged in a comfortable hotel at very special rates. The conference room (in the same hotel) is air-conditioned and equipped with all conference materials. Special areas are reserved to students for the afternoon coursework and study. The island of Lipari can be easily reached from Milazzo, Palermo, Naples, Messina and Reggio Calabria by ferry or hydrofoil (50 minutes from Milazzo). Two kinds of participants are welcome. Students: Participants who are expected to do afternoon courseworks and take a final exam (The grades will be given following the ECTS grading scale). The course will involve a total of 24 hours of teaching. According to our university rules passing the final exam gives right to an equivalent of 6 ECTS credits in any Ph.D. program. Auditors: participants who are not interested in taking the final exam. Registration fee is 450 Euros. The fee covers the course material, bus+hydrofoil Catania airport-Lipari-Catania airport, social event. Late registration is 550 Euros. Deadline for application is May 1, 201. Applicants must include a short curriculum vitae and specify two professors whom letters of recommendation will be asked to, if deemed necessary. Applicants will be notified about admission by May 10, 2011. The official language is English. School Directors * Prof. Alfredo Ferro (University of Catania) * Prof. Raffaele Giancarlo (University of Palermo) * Prof. Concettina Guerra (University of Padova and Georgia Tech.) * Prof. Michael Levitt, (Stanford University) * Dr. Rosalba Giugno (co-director, University of Catania) * Dr. Alfredo Pulvirenti (co-director, University of Catania) People interested in receiving further information about the school can contact: Lipari School Organization Prof. Alfredo Ferro -- Susanna Caramello (Lipari School secretary) Universita' degli Studi di Catania - Dipartimento di Matematica e Informatica Citta' Universitaria - Viale A.Doria, 6 - 95125 Catania - ITALY Tel: +39 095 7383071 Fax: +39 095 7337032 / +39 095 330094 E-mail:school at dmi.unict.it - susanna at dmi.unict.it From witch_of_agnessi at yahoo.com Fri Feb 4 13:51:09 2011 From: witch_of_agnessi at yahoo.com (Skull Crossbones) Date: Fri, 4 Feb 2011 10:51:09 -0800 (PST) Subject: [BiO BB] On searching Refseq_mrna database Message-ID: <91286.56244.qm@web110016.mail.gq1.yahoo.com> I wish to do a tblastx search against the Refseq_mrna database. However I'm sceptical about searching the database in all six reading frames.For protein coding mRNAs will it be more appropriate to search the database in frame 1 only? as the mrna sequence will correspond to the protein coding region. Thanks in advance From jprudhomme at healthtech.com Mon Feb 7 07:24:51 2011 From: jprudhomme at healthtech.com (Jim Prudhomme) Date: Mon, 7 Feb 2011 07:24:51 -0500 Subject: [BiO BB] CHI's Structure-Based Design Conference Message-ID: <044a01cbc6c2$04bb9b30$0e32d190$@com> ** Please distribute this conference announcement to those who may be interested.** ============================== Final Conference Agenda Just Posted! ============================== Cambridge Healthtech Institute and Bio-IT World Present the Eleventh Annual STRUCTURE-BASED DRUG DESIGN June 6-8, 2011 Royal Sonesta Boston Hotel - Cambridge, MA http://www.healthtech.com/sbd Conference Highlights: * Protein Flexibility * Fully Synthetic Protein-Protein Interaction Inhibitor * Fragment-to-Lead Optimization * High Performance Computing and Collaborative Drug Design * State-of-the-Art Molecular Dynamics Simulations Keynote Speaker: Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine David E. Shaw, Ph.D., Chief Scientist, D. E. Shaw Research Dinner Short Course:* June 8, 2011 Identification of Druggable Sites for Protein-Protein Interaction Targets How to Register: Web: https://chidb.com/register/2011/sbd/reg.asp Call: +1 781-972-5400 For details on sponsorship and exhibit opportunities, contact: Katelin Fitzgerald, +1 781-972-5458, kfitzgerald at healthtech.com For details on group discounts, contact: David Cunningham, +1 781-972-5472, cunningham at healthtech.com *Separate registration is required to attend the dinner short course. James Prudhomme Marketing Manager Cambridge Healthtech Institute 250 First Avenue, Suite 300 Needham, MA 02494 Direct: 781-972-5486 Fax: 781-972-5425 www.healthtech.com From boris.steipe at utoronto.ca Mon Feb 7 09:29:05 2011 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Mon, 7 Feb 2011 09:29:05 -0500 Subject: [BiO BB] On searching Refseq_mrna database In-Reply-To: <91286.56244.qm@web110016.mail.gq1.yahoo.com> References: <91286.56244.qm@web110016.mail.gq1.yahoo.com> Message-ID: Dear Anonymous, The point of these searches is to retrieve matches that might not be recognizable after conceptual translation because of frameshifts or gene-model errors in query and/or subject. For this reason, you would not search m-RNA in six frames to begin with, but you would use genomic DNA (or preliminary datasets from genome sequencing assemblies). Best, Boris On 2011-02-04, at 1:51 PM, Skull Crossbones wrote: > I wish to do a tblastx search against the Refseq_mrna database. However I'm sceptical about searching the database in all six reading frames.For protein coding mRNAs will it be more appropriate to search the database in frame 1 only? as the mrna sequence will correspond to the protein coding region. > > Thanks in advance > > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From Robin.Haw at oicr.on.ca Mon Feb 7 20:01:01 2011 From: Robin.Haw at oicr.on.ca (Robin Haw) Date: Mon, 7 Feb 2011 20:01:01 -0500 Subject: [BiO BB] Reactome Pathway Database User Survey Message-ID: We appreciate your assistance in evaluating Reactome. Your responses will give us an indication of the effectiveness of the Reactome website and tools, and areas in which improvement could be made. We would like to know a bit about your background and research interests and welcome your written comments and suggestions. The survey should take about 5 minutes to complete. The information you provide will never be made publicly available or shared with third parties. Participation in the survey is optional. However, five lucky participants who complete the survey will receive a Reactome T-shirt. You can access the survey at: https://www.surveymonkey.com/s/RV63355 Thank you for taking part. Regards, Robin Haw Robin Haw, PhD Scientific Associate Manager of Reactome Outreach Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 ?????? Tel: ????????647-260-7985 Toll-free: 1-866-678-6427 http://www.oicr.on.ca http://www.reactome.org This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization. From jeff at bioinformatics.org Wed Feb 9 11:25:42 2011 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Wed, 09 Feb 2011 11:25:42 -0500 Subject: [BiO BB] Bifx Africa-India Virtual Conference 2011 Message-ID: <4D52C006.5030504@bioinformatics.org> REGISTER TODAY FOR AS LITTLE AS $10 USD! Bifx Africa-India Joint Virtual Conference 2011 February 10-11, 2011 Online at Bioinformatics.Org http://www.bioinformatics.org/wiki/Bifx11 Agenda: http://mat.edu.bioinformatics.org/BIFX11/Bifx11-Agenda.pdf Abstract booklet: http://mat.edu.bioinformatics.org/BIFX11/Bifx11-Booklet.pdf The Bifx Africa-India Joint Virtual Conference 2011 (Bifx11) follows on the success of Bifx09 and Bifx10. This joint conference is organized by Bioinformatics.Org, Bioclues.org, and the African Society of Bioinformatics and Computational Biology (ASBCB). SPEAKERS: * Sharmila Bapat, Scientist, National Centre for Cell Science, Pune, India: Systems Networks and Cancer Research * Junaid Gamieldien, Lecturer, South African National Bioinformatics Institute: Semantic Integration of Biomedical Knowledge and Existing Data to Support In-Silico Discovery * Lalji Singh, CSIR Bhatnagar fellow, Centre for Cellular and Molecular Biology, Hyderabad, India * Simon Travers, Associate Professor, South African National Bioinformatics Institute * Jayaraman Valadi Scientist Emeritus-CSIR, India and APBioNet.org-India representative and Arun Gupta CEO, AbhyudayaTech: Support Vector Machines: Applications and Challenges in Bioinformatics WITH MORE THAN A DOZEN STUDENT PRESENTATIONS! HOW TO REGISTER: The registration fee has been set very low to increase attendance from students and those in developing nations. Please visit: http://www.bioinformatics.org/wiki/Bifx11#Registration Please contact edu at bioinformatics.org if you have any questions about registration. Waivers are available if your country doesn't permit PayPal payments. Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 621 8258 -- From isbra-l at dna.engr.uconn.edu Wed Feb 9 12:12:53 2011 From: isbra-l at dna.engr.uconn.edu (International Symposium on Bioinformatics Research and Applications) Date: Wed, 9 Feb 2011 12:12:53 -0500 Subject: [BiO BB] [ISBRA-L] ISBRA'11 CFP -- submission deadline Friday, Feb. 11, 2011 Message-ID: CALL FOR PAPERS 7th International Symposium on Bioinformatics Research and Applications May 27-29, 2011 Central South University, Changsha, China http://www.cs.gsu.edu/isbra/ 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 * Biomolecular imaging * Bio-ontologies * Comparative genomics * Computational genetic epidemiology * Computational proteomics * Data mining and visualization * Gene expression analysis * Genome analysis * High-performance bio-computing * High-throughput sequencing data analysis * Molecular evolution * Molecular modeling and simulation * Pattern discovery and classification * Population genetics * Software tools and applications * Structural biology * 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=isbra2011i. 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 series and presented orally at the symposium. Accepted short abstracts will be published online and on CD-ROM and selected for either oral or poster presentation. As in previous years, 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. The authors of remaining extended and short abstracts will be invited to submit full versions to a peer-reviewed volume to be published after the symposium in BMC Bioinformatics. IMPORTANT DATES Extended Abstracts Short Abstracts (12 pages) (4 pages) Submission deadline February 11, 2011 April 8, 2011 Notification of acceptance March 11, 2011 April 22, 2011 Final version due March 18, 2011 April 29, 2011 KEYNOTE SPEAKERS Bernard Moret (EPFL) David Sankoff (Univ. of Ottawa) Russell Schwartz (Carnegie Mellon) Liping Wei (Peking University) Eric Xing (Carnegie Mellon STEERING CHAIRS Dan Gusfield (UC Davis) Yi Pan (Georgia State) Marie-France Sagot (INRIA) GENERAL CHAIRS Mona Singh (Princeton) Lijian Tao (Central South University) Albert Y. Zomaya (University of Sydney) PROGRAM CHAIRS Jianer Chen (Texas A&M) Jianxin Wang (Central South University) Alexander Zelikovsky (Georgia State) -------------- next part -------------- _______________________________________________ ISBRA-L mailing list ISBRA-L at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/isbra-l From fabrizio.sebastiani at isti.cnr.it Fri Feb 11 05:04:19 2011 From: fabrizio.sebastiani at isti.cnr.it (Fabrizio Sebastiani) Date: Fri, 11 Feb 2011 11:04:19 +0100 Subject: [BiO BB] Call for Papers: SPIRE 2011 Message-ID: Call for Papers 18th Symposium on String Processing and Information Retrieval (SPIRE 2011) Pisa, Italy October 17--21, 2011 http://spire2011.isti.cnr.it/ SPIRE 2011 is the 18th edition of the International Symposium on String Processing and Information Retrieval. It will will take place at the National Council of Research campus (?Area della Ricerca del CNR?) in Pisa, Italy, and will be co-organized by the Institute for the Science and Technologies of Information of the Italian National Council of Research (ISTI-CNR), Pisa, and the Department of Computer Science of the University of Pisa. The scope of the SPIRE series of symposia includes not only fundamental algorithms in string processing and information retrieval, but also SP and IR techniques as applied to areas such as computational biology, DNA sequencing, and Web mining. Given its interdisciplinary nature, SPIRE offers a unique opportunity for researchers from these different areas to meet and network. Typical topics of interest include, but are not limited to: * String Processing: Dictionary algorithms, Text searching, Pattern matching, Text and sequence compression, Succinct and compressed indexing, Automata-based string processing; * Biological Sequence Processing: Analysis of DNA and RNA sequencing data, Molecular sequence processing, Recognition of genes and regulatory elements, Comparative genomics and population genetics; * Information Retrieval: Information retrieval models, Indexing, Ranking and filtering, Interface design for IR, Evaluation issues in IR, Text analysis, Text mining, Text classi fication and clustering, Information extraction, Language models and topic models for search related-tasks, Efficient implementation of IR systems, Algorithms and data structures for IR; * Search-related tasks: Cross-lingual information retrieval, Multimedia / multi-modal information retrieval, Recommendation and collaborative filtering, Semi-structured data retrieval, Blog retrieval. SPIRE 2011 welcomes either long papers (12 pages) or short papers (6-pages). Submissions must be anonymous and formatted using the Springer LNCS style. At least three reviewers will evaluate each paper in double-blind mode based on its originality, quality, methodological robustness, and significance of theoretical and/or practical contribution. Papers must be in English, must be unpublished, and must not be under submission at another conference or journal for the entire duration of the SPIRE 2011 reviewing process. All papers will be refereed according to the usual scientific standards. Accepted papers will appear in the Proceedings published by Springer Verlag in the Lecture Notes in Computer Science series, which will be distributed to all delegates at the symposium. SPIRE 2011 will also feature a full day of tutorials and a full day of workshops. See http://spire2011.isti.cnr.it/ if you are interested in submitting either a tutorial or a workshop proposal. SPIRE 2011 General Chair Fabrizio Sebastiani, National Council of Research, IT SPIRE 2011 Program Chairs Roberto Grossi, University of Pisa, IT Fabrizio Silvestri, National Council of Research, IT SPIRE 2011 Program Committee - To be announced - Important Dates Paper Submission: April 20, 2011 Accept/Reject notification: June 15, 2011 Camera-ready copy due: July 15, 2011 Conference: October 17-21, 2011 From sandra.gesing at uni-tuebingen.de Fri Feb 11 07:41:37 2011 From: sandra.gesing at uni-tuebingen.de (Sandra Gesing) Date: Fri, 11 Feb 2011 13:41:37 +0100 Subject: [BiO BB] IWSG-Life (International Workshop on Science Gateways for Life Sciences), June 8-10 2011, London, UK Message-ID: <20110211134137.14527cfj27buq0e9@webmail.uni-tuebingen.de> Dear all, I would appreciate if you would forward the CALL FOR PAPERS to projects which may be interested. Thanks, Sandra Gesing ------------------------------------------------------------- (Apologies for multiple cross-postings) IWSG-Life 2011 (3rd International Workshop on Science Gateways for Life Sciences) Workshop Website: http://www.cpc.wmin.ac.uk/iwsg2011 Date: 8-10 June 2011 Place: University of Westminster, London, UK Important dates: Deadline for paper/abstract submission: 1st April 2011 Notification of acceptance: 22nd April 2011 Submission of camera ready papers: 13 May 2011 Registration deadline: 27 May 2011 Date of the workshop: 8-10 June 2011 Scope: IWSG-Life'11 will bring together scientists from the field of life sciences, bioinformatics and computer science. The aim is to exchange experience, formulate ideas and introduce up-to-date technological advances in molecular and systems biology in the context of Science Gateways. We invite the submission of papers related to various aspects of molecular and systems biology and Science Gateways/Portals. Suggested topics include, but are not limited to: " Management of biological high-throughput data " Modeling protein-carbohydrate recognition " Machine learning for computational immunomics " Molecular simulations for drug discovery " Portal technology and portal construction methods " Usage models and gateway tools for life sciences " Security aspects of Science Gateways for life sciences " Usability studies of life sciences portals/gateways " Workflows and service composition for life sciences " Service discovery and ontologies for life sciences " Tools for managing grid and cloud portability " Integration of life sciences with e-infrastructures " Demonstrations/ success stories Call for papers There are three alternatives for researchers to present their work: talks, lightning talks, and demonstration sessions. Submission of a full paper may result in a talk, submission of an abstract may result in an lightning talk or a demonstration. Authors of best papers will be invited to submit a significantly extended and updated version of their paper into the Journal of Grid Computing for a Special Issue on Science Gateways. Full papers All full papers will be double-blind peer reviewed and evaluated on quality and relevance. All submissions are held in confidentiality prior to publication in the proceedings. Accepted full papers will be published as open access, online-only workshop proceedings and will result in fully citable articles. The proceedings will be available online approximately one week prior to the workshop opening. Presenters will be given a 20-minute time slot (plus 5 minutes for questions) to provide a summary and update to their work. Papers will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site. They have to be formatted according to the layout style required by the OUP bioinformatics journal. Formatting requirements can be found at: http://www.oxfordjournals.org/bioinformatics/for_authors/submission_online.html. The paper length must not exceed eight pages and the papers must be written in clear and readably English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. Abstracts Abstracts can be submitted for the lightning talk or for the demonstration sessions. Authors must indicate clearly which presentation format they are aiming for. All abstracts will be double-blind peer reviewed and evaluated on quality and relevance. Accepted lightning talk submissions will be given a 10-minute time slot (plus 5 minutes for questions) in an lightning talk session. Accepted demonstration submissions will be given a 10-minute time slot (plus 5 minutes for questions) in a demonstration session. Demonstrations will be given live to the workshop audience. Abstracts will be accepted electronically in PDF format only and are to be submitted through our EasyChair conference site. The abstract length must not exceed 200 words and the abstracts must be written in clear and readably English. Every accepted submission must register and pay for at least one person. We expect one of the authors to attend the workshop and present the work. -- The University of Westminster is a charity and a company limited by guarantee. Registration number: 977818 England. Registered Office: 309 Regent Street, London W1B 2UW, UK. From hlapp at gmx.net Wed Feb 16 18:01:42 2011 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 16 Feb 2011 18:01:42 -0500 Subject: [BiO BB] Call for Abstracts open for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) Message-ID: <60DE2847-19AC-4E68-9324-A5B82AD7D139@gmx.net> The Call for Abstracts for full talks is now open for the 2011 conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio), at http://ievobio.org/ocs/index.php/ievobio/2011. See below for instructions. Accepted talks will be about 15-20 minutes in length and will be presented during the full talk sessions in the morning of each of the two conference days, following the day's keynote presentation. 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. As the number of program slots for full talks is limited, the abstract should give enough detail so reviewers can decide whether the submission merits a full talk or whether it should be moved to one of the Lightning Talk sessions. If the subject of the talk is a specific software component for use by the research community, the abstract must state the license and give the URL where the source code is available so reviewers can verify that the open-source requirement(*) is met. The deadline for submission is March 18, 2011. We intend to notify authors of accepted talks before early registration for iEvoBio (and Evolution) ends. Further instructions for submission are at the following URL: http://ievobio.org/ocs/index.php/ievobio/2011/schedConf/cfp Full talks are 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 already open (see http://ievobio.org/challenge.html). The calls for contribution to the other 3 sessions will open later, and will remain open until shortly before the conference or until the respective track fills up. 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 , or subscribe to the low-traffic iEvoBio announcements mailing list at http://groups.google.com/group/ievobio-announce iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) (*) 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. Authors of full talks who cannot meet this requirement at the time of submission should state their intentions, and are advised that the requirement must be met by June 19, 2011, at the latest. From gary.bader at utoronto.ca Thu Feb 17 10:02:22 2011 From: gary.bader at utoronto.ca (Gary Bader) Date: Thu, 17 Feb 2011 10:02:22 -0500 Subject: [BiO BB] The BioPAX pathway data standard community survey Message-ID: <86B3B7AA-39D5-4C58-AC49-6EBA4320EA76@utoronto.ca> BioPAX is a standard language for representing and exchanging information about biological pathways. BioPAX Level 3 supports metabolic and signaling pathways and gene regulation, molecular and genetic interactions. We are seeking your input on what the BioPAX community should work on next. Should we focus on making more data available, software support or new features in BioPAX that enable more data to be captured? Please let us know! Your answers will be used to make decisions about next steps at the BioPAX meeting in New York in mid-April 2011. Please reply to this survey as soon as you can, and no later than March 30th, 2011. The survey can be found here: http://www.surveymonkey.com/s/GR3MMJM Individual responses will be kept confidential. Many Thanks, The BioPAX team www.biopax.org If you are on multiple mailing lists, you may receive this e-mail more than once, our apologies. From clementsgalaxy at gmail.com Tue Feb 22 12:31:23 2011 From: clementsgalaxy at gmail.com (Dave Clements) Date: Tue, 22 Feb 2011 09:31:23 -0800 Subject: [BiO BB] Galaxy Community Conference, May 25-26, Lunteren, The Netherlands In-Reply-To: References: Message-ID: Hello all, Just a reminder that the abstract submission deadline for the Galaxy Community Conference is next Monday, February 28. See http://galaxy.psu.edu/gcc2011/Abstracts.html for details. Cheers, Dave C. PS: And there is still space at the GMOD Meeting being held March 5-6 @ NESCent: http://gmod.org/wiki/March_2011_GMOD_Meeting On Thu, Feb 3, 2011 at 5:25 PM, Dave Clements wrote: > We are pleased to announce the *2011 Galaxy Community Conference*, being > held *May 25-26 in Lunteren, The Netherlands*. The meeting will feature > two full days of presentations and discussion on extending Galaxy to use new > tools and data sources, deploying Galaxy at your organization, and best > practices for using Galaxy to further your own and your community's > research. See http://galaxy.psu.edu/gcc2011/ for complete details. > > *About Galaxy: > *Galaxy is an open, web-based platform for *accessible, reproducible, and > transparent* computational biomedical research. > > - *Accessibility:* Galaxy enables users without programming experience > to easily specify parameters and run tools and workflows. > - *Reproducibility:* Galaxy captures all information necessary so that > any user can repeat and understand a complete computational analysis. > - *Transparency:* Galaxy enables users to share and publish analyses > via the web and create Pages--interactive, web-based documents that describe > a complete analysis. > > Galaxy is open source for all organizations. The public Galaxy service ( > http://usegalaxy.org) makes analysis tools, genomic data, > tutorial demonstrations, persistent workspaces, and publication services > available to any scientist that has access to the Internet. Local > Galaxy servers can be set up by downloading the Galaxy application and > customizing it to meet particular needs. > > *Conference Overview: > * > This event aims to engage a broader community of developers, data > producers, tool creators, and core facility and other research hub staff to > become an active part of the Galaxy community. We'll cover defining > resources in the Galaxy framework, increasing their visibility and making > them easier to use and integrate with other resources, how to extend Galaxy > to use custom data sources and custom tools, and best practices for using > Galaxy in your organization. > > Additional topics include, but are not limited to: > * Talks submitted by the Galaxy community > * Integration of tools (including NGS analysis tools) and distributed job > management > * Deployment of Galaxy instances on local resources and on the Cloud > * Management of large datasets with the Galaxy Library System > * Using the Galaxy LIMS functionality at NGS sequencing facilities > * Visualizing Data without leaving Galaxy > * Performing reproducible research > * Performing and sharing complex analyses with Workflows > * An "Introduction to Galaxy" session, offered on May 24, for Galaxy > newcomers. > > *Registration: > * > The conference fee is ?100 on or before April 24, and ?120 after that. The > meeting is being held at the Conference Centre De Werelt in Lunteren, The > Netherlands, which is also the conference hotel. You are encouraged to > register early, as space at the hotel (and at the "Intro to Galaxy" session) > is limited and is likely to fill up before the conference itself does. See > http://galaxy.psu.edu/gcc2011/Register.html > * > Abstract Submission: > * > Abstracts are now being accepted for short oral presentations. Proposals > on any topic of interest to the Galaxy community are welcome and > encouraged. The abstract submission deadline is the end of February 28. > See http://galaxy.psu.edu/gcc2011/Abstracts.html > * * > *Sponsors > * > The 2011 Galaxy Community Conference is co-sponsored by the US National > Science Foundation (NSF, http://www.nsf.gov/), and the Netherlands > Bioinformatics Centre (NBIC, http://www.nbic.nl/). NBIC is a > collaborative institute of the bioinformatics groups in the Netherlands. > Together, these groups perform cutting-edge research, develop novel tools > and support platforms, create an e-science infrastructure and educate the > next generations of bioinformaticians. > > We are looking forward to a great conference and hope to see you in the > Netherlands! > > The Galaxy and NBIC Teams > > -- > http://galaxy.psu.edu/gcc2011/ > http://getgalaxy.org > http://usegalaxy.org/ > -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ From idoerg at gmail.com Wed Feb 23 15:40:27 2011 From: idoerg at gmail.com (Iddo Friedberg) Date: Wed, 23 Feb 2011 15:40:27 -0500 Subject: [BiO BB] Fwd: Automated Function Prediction SIG: Call for Abstracts In-Reply-To: References: Message-ID: Please forward as appropriate. Locale Vienna, Austria Dates: July 15-16, 2011 URL: http://biofunctionprediction.org Important dates: April 18, 2011: Deadline for submitting extended abstracts. May 9, 2011: Notifications for accepted abstracts e-mailed to corresponding authors May 16, 2011: Deadline for presenters to confirm acceptance of invitation to speak. July 15-16, 2011: AFP SIG alongside ISMB 2011 An ISMB Special Interest Group Meeting Automated Protein Function Prediction featuring CAFA: Critical Assessment of Function Annotations Sequence and structure genomics have generated a wealth of data, but extracting meaningful information from genomic information is becoming an increasingly difficult challenge. Both the number and the diversity of discovered sequences are increasing, while the fraction of genes whose function is known is decreasing.In addition, there is a need for annotation which is standardized so that it could be incorporated into function annotation on a large scale. Finally, there is a need to assess the quality of the function prediction software which is out there. For these reasons and many more, automated protein function prediction is rapidly gaining interest among computational biologists in academia and industry. The AFP SIG has been part of ISMB since 2005. This year the AFP SIG will feature CAFA: Critical Assessment of Function Annotations. Over 30 research groups from around the world are participating in CAFA. In late 2010, these groups have used computational tools to predict the function for a large set of protein sequences. The accuracy of these predictions will be assessed at this year's AFP meeting. We call upon all researchers involved in gene and protein function prediction to submit an abstract to the AFP meeting. Authors of selected abstracts will be invited to give a talk and/or present a poster. Select authors will also be invited to write a full paper which will be considered for publication in a peer-reviewed scientific journal. For further instructions on how to submit abstracts to AFP/CAFA, please go here: http://biofunctionprediction.org/node/415 We are looking forward to seeing you in Vienna! Iddo Friedberg, Michal Linial and Predrag Radivojac The AFP organizing committee -- Iddo Friedberg http://iddo-friedberg.net/contact.html From tirza at biomodel.os.biu.ac.il Thu Feb 24 07:20:24 2011 From: tirza at biomodel.os.biu.ac.il (Tirza Doniger) Date: Thu, 24 Feb 2011 14:20:24 +0200 Subject: [BiO BB] List of brain related genes Message-ID: Hi, I am look for a list of genes that are human brain/neurological specific. Can I find this information in the GO database? What other sources are available? Thanks, Tirza -- Tirza Doniger, Ph.D. Bioinformatics Unit The Mina and Everard Faculty of Life Sciences Bar Ilan University ====================== From s_uchida21 at yahoo.co.jp Thu Feb 24 23:36:16 2011 From: s_uchida21 at yahoo.co.jp (=?ISO-2022-JP?B?GyRCRmJFRBsoQiAbJEJMdzpIGyhC?=) Date: Fri, 25 Feb 2011 13:36:16 +0900 (JST) Subject: [BiO BB] List of brain related genes In-Reply-To: Message-ID: <20110225043616.10082.qmail@web2503.mail.tnz.yahoo.co.jp> Dear Tirza: Hello. We have built a knowledge database that fits your needs: "C-It": http://c-it.mpi-bn.mpg.de/ You can find more info from our recent publication in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/26/18/2328.abstract Shizuka ************************************************* Dr. Shizuka Uchida, PhD Max-Planck-Institute for Heart and Lung Research Dept. of Cardiac Development and Remodelling W.G. Kerckhoff-Institute Ludwigstr. 43 61231 Bad Nauheim phone: +496032/705-1107 fax: +496032/705-1104 E-mail. Shizuka.Uchida at mpi-bn.mpg.de Homepage: http://www.mpi-hlr.de/index.php?id=455&L=1 ************************************************* Tirza Doniger wrote: Hi, I am look for a list of genes that are human brain/neurological specific. Can I find this information in the GO database? What other sources are available? Thanks, Tirza -- Tirza Doniger, Ph.D. Bioinformatics Unit The Mina and Everard Faculty of Life Sciences Bar Ilan University ====================== _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From s_uchida21 at yahoo.co.jp Thu Feb 24 23:36:16 2011 From: s_uchida21 at yahoo.co.jp (=?ISO-2022-JP?B?GyRCRmJFRBsoQiAbJEJMdzpIGyhC?=) Date: Fri, 25 Feb 2011 13:36:16 +0900 (JST) Subject: [BiO BB] List of brain related genes In-Reply-To: Message-ID: <20110225043616.10082.qmail@web2503.mail.tnz.yahoo.co.jp> Dear Tirza: Hello. We have built a knowledge database that fits your needs: "C-It": http://c-it.mpi-bn.mpg.de/ You can find more info from our recent publication in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/26/18/2328.abstract Shizuka ************************************************* Dr. Shizuka Uchida, PhD Max-Planck-Institute for Heart and Lung Research Dept. of Cardiac Development and Remodelling W.G. Kerckhoff-Institute Ludwigstr. 43 61231 Bad Nauheim phone: +496032/705-1107 fax: +496032/705-1104 E-mail. Shizuka.Uchida at mpi-bn.mpg.de Homepage: http://www.mpi-hlr.de/index.php?id=455&L=1 ************************************************* Tirza Doniger wrote: Hi, I am look for a list of genes that are human brain/neurological specific. Can I find this information in the GO database? What other sources are available? Thanks, Tirza -- Tirza Doniger, Ph.D. Bioinformatics Unit The Mina and Everard Faculty of Life Sciences Bar Ilan University ====================== _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From bsmagic at gmail.com Fri Feb 25 21:45:55 2011 From: bsmagic at gmail.com (Sheng Wang) Date: Sat, 26 Feb 2011 10:45:55 +0800 Subject: [BiO BB] List of brain related genes In-Reply-To: References: Message-ID: maybe you could find some helpful information on some brain relate microarray database an publications. -- Best Regards, *Sheng Wang* bsmagic at gmail.com 2011/2/24 Tirza Doniger > Hi, > > I am look for a list of genes that are human brain/neurological specific. > Can I find this information in the GO database? What other sources are > available? > > Thanks, > Tirza > > -- > Tirza Doniger, Ph.D. > Bioinformatics Unit > The Mina and Everard Faculty of Life Sciences > Bar Ilan University > ====================== > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From maximilianh at gmail.com Fri Feb 25 04:03:43 2011 From: maximilianh at gmail.com (Maximilian Haussler) Date: Fri, 25 Feb 2011 09:03:43 +0000 Subject: [BiO BB] List of brain related genes In-Reply-To: References: Message-ID: If you need specific genes, you can try an insitu database like eurexpress or mouse expression data from MGI. You can download where genes are expressed and then filter the gene lists. cheers Max On Thu, Feb 24, 2011 at 12:20 PM, Tirza Doniger wrote: > Hi, > > I am look for a list of genes that are human brain/neurological specific. > Can I find this information in the GO database? What other sources are > available? > > Thanks, > Tirza > > -- > Tirza Doniger, Ph.D. > Bioinformatics Unit > The Mina and Everard Faculty of Life Sciences > Bar Ilan University > ====================== > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From neha.chaudhary1685 at gmail.com Fri Feb 25 04:44:55 2011 From: neha.chaudhary1685 at gmail.com (Neha Chaudhary) Date: Fri, 25 Feb 2011 10:44:55 +0100 Subject: [BiO BB] Request for help Message-ID: Hiiii, I have done my masters in bioinformatics with little knowledge of programming and statistics. I am working on metabolic network - basically metabolic flux analysis. The basic idea which I had started with was the comparison of the metabolic space of two organisms by picking up flux distribution points using monte carlo randomly and then comparing them. I am in a lab which works in wet lab only and doesnt have much idea about computational biology. I cant clear my way ahead as to how to proceed with the work. Any body who is has knowledge and is interested in systems biology, plz help me. Regards Neha - From cannataro at unicz.it Fri Feb 25 13:10:34 2011 From: cannataro at unicz.it (Mario Cannataro) Date: Fri, 25 Feb 2011 19:10:34 +0100 (CET) Subject: [BiO BB] CBMS 2011 - Computational Proteomics and Genomics Special Track In-Reply-To: <8714cc3a577511f1aa9ad468b57a60fe.squirrel@email.unicz.it> References: <503239aa165f7384cfd05fe975b6d169.squirrel@email.unicz.it> <8714cc3a577511f1aa9ad468b57a60fe.squirrel@email.unicz.it> Message-ID: 24th IEEE International Symposium on COMPUTER-BASED MEDICAL SYSTEMS June 27th - 30th, University of the West of England, Bristol, UK 6th Special Track Computational Proteomics and Genomics: Management and Analysis of ?omics? Data http://staff.icar.cnr.it/cannataro/cbms2011 CALL FOR PAPERS 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 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. The integrated application of bioinformatics methods to clinical data is at the basis of Translational Research and Translational Medicine, whose goals is to translate the findings in basic research into medical practice. Wang and Liotta recently introduced the concept of Clinical Bioinformatics, i.e. "clinical application of bioinformatics-associated sciences and technologies to understand molecular mechanisms and potential therapies for human diseases", as a new and important concept for the development of disease-specific biomarkers and individualized medicine. 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 translational research and medicine. 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 Translational Medicine and 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 genomics and proteomics in translational medicine and 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 contribution must be prepared following the IEEE 2-column format format, and should not exceed the length of 6 (six) Letter-sized pages; the authors may use LaTeX or Microsoft Word templates when preparing their drafts. The papers should be submitted electronically before the paper submission deadline using the EasyChair online submission system. Papers must be submitted in PDF format, with fonts embedded. Authors of accepted papers should refer to the full IEEE Xplore? PDF Specification. All submissions will be peer-reviewed by at least three reviewers. All accepted papers will be included in the conference proceedings published by the IEEE CS Press. At least one author must pay the registration fee before May 30th for each accepted paper. Please refer to the IEEE IPR guidelines concerning copyright. Authors of accepted papers must include a completed IEEE Copyright Form with the submission of their final camera-ready paper. Please contact cannataro AT unicz DOT it for any question. IMPORTANT DATES Paper submission deadline: 20 April 2011 Notification of acceptance for papers: 20 May 2011 Final camera ready due: 30 May 2011 Author registration: 30 May 2011 JOURNAL SPECIAL ISSUE After the workshop, selected papers may be invited for a special issue of an international journal. Selected papers (extended and revised versions) accepted on the previous editions of the workshop have been published on a special section of Briefings in Bioinformatics (Oxford University Press). 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, SystemsX.ch, 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 dostone at gmail.com Fri Feb 25 13:54:13 2011 From: dostone at gmail.com (Eric Lei Du) Date: Fri, 25 Feb 2011 13:54:13 -0500 Subject: [BiO BB] List of brain related genes In-Reply-To: <20110225043616.10082.qmail@web2503.mail.tnz.yahoo.co.jp> References: <20110225043616.10082.qmail@web2503.mail.tnz.yahoo.co.jp> Message-ID: Hi, Shizuka, C-It is wonderful. Is it offering flatfile download for academic use? Thanks. Eric --------------------------------- Harbin Medical Univerisity Harbin 150081 China --------------------------------- 2011/2/24 ?? ?? : > Dear Tirza: > > ?Hello. We have built a knowledge database that fits your needs: > > ?"C-It": ?http://c-it.mpi-bn.mpg.de/ > > ?You can find more info from our recent publication in Bioinformatics: > > ?http://bioinformatics.oxfordjournals.org/content/26/18/2328.abstract > > ?Shizuka > > ? ?************************************************* > Dr. Shizuka Uchida, PhD ? Max-Planck-Institute > for Heart and Lung Research > Dept. of Cardiac Development and Remodelling > W.G. Kerckhoff-Institute > Ludwigstr. 43 > 61231 Bad Nauheim > phone: ? ? ? +496032/705-1107 > fax: ? ? ? ? ? ?+496032/705-1104 > E-mail. Shizuka.Uchida at mpi-bn.mpg.de > ?Homepage: ?http://www.mpi-hlr.de/index.php?id=455&L=1 > > ?************************************************* > > > Tirza Doniger wrote: > ?Hi, > > I am look for a list of genes that are human brain/neurological specific. > Can I find this information in the GO database? What other sources are > available? > > Thanks, > Tirza > > -- > Tirza Doniger, Ph.D. > Bioinformatics Unit > The Mina and Everard Faculty of Life Sciences > Bar Ilan University > ====================== > _______________________________________________ > 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 ljgarcia at ebi.ac.uk Mon Feb 28 06:51:43 2011 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Mon, 28 Feb 2011 11:51:43 +0000 Subject: [BiO BB] Graphical representation for protein annotations Message-ID: <4D6B8C4F.4080200@ebi.ac.uk> Dear all, I need to know if there is a key of colours and shapes for the graphical representation of annotations in proteins. for instance, if I need to have a pictorial representation of a "domain" or "transcript" then is there a standardized way to do it? So far I have seen that domains are usually represented as ellipses or rectangles, and metal bindings as non-filled circles, while active sites are red-filled circles. I am particular interested in the next type of annotations: Domain, Signal, Transit, Propeptide, Peptide, Topological domain, Intramembrane, Transmenbrane for ranges of sequences, and Metal binding, Active site, Modified residue, Lipidation, Glycosilation for point positions. I appreciate any information on this matter. Cheers, Leyla Garc?a EMBL-EBI, Cambridge, UK From apico at gladstone.ucsf.edu Mon Feb 28 13:31:56 2011 From: apico at gladstone.ucsf.edu (Alexander Pico) Date: Mon, 28 Feb 2011 10:31:56 -0800 Subject: [BiO BB] Call for Abstracts : Network Biology SIG at ISMB 2011 in Vienna, July 15th In-Reply-To: Message-ID: Call for Abstracts: Network Biology SIG at ISMB 2011 in Vienna DATE CHANGED TO: July 15th The Network Biology (NetBio) SIG will focus on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology, synthetic biology and medicine. The meeting will provide a unique interface between tool developers and users in the field of network biology. Through these complementary lenses, the SIG will bring into focus the current state of the field, its future promise and how to get there. http://nrnb.org/netbiowiki == Keynote speakers == Trey Ideker, ?Rewiring of Genetic Networks by DNA Damage? ? ???University of California at San Diego Alfonso Valencia, ?Using and Completing Cancer Networks? ???Spanish National Cancer Research Centre Gary Bader, ?Network and Pathway Information: Collecting, visualizing and using for gene function prediction? ???University of Toronto Henning Hermjakob, ?Reactome, IntAct, PSICQUIC: Bringing pathways and interactions together? ????European Bioinformatics Institute (EBI) == Call for Abstracts == We invite abstracts for talks at one of the two main sessions: Tools & Resources or Applied Research. We are seeking a diversity of submissions to represent the breadth and depth of Network Biology. Find guidelines at http://nrnb.org/netbiowiki/Abstract_submission == Important Details == Date: July 15, 2011 Location: Vienna, Austria ISMB site: http://www.iscb.org/ismbeccb2011-program/satellite-meetings#network NetBio wiki: http://nrnb.org/netbiowiki Mailing list: http://groups.google.com/group/netbio Abstract submission: http://nrnb.org/netbiowiki/Abstract_submission == Important Dates == Feb 7: Open for submissions April 8: Abstract deadline April 29: Notification of accepted abstracts July 15: NetBio SIG 2011 See you there! NetBio Organizing Committee Alexander Pico (apico at gladstone.ucsf.edu), Scooter Morris, Allan Kuchinsky, Annette Adler, Gary Bader, Mario Albrecht, Diego di Bernardo, Ian Donaldson, Hana El-Samad