Call for Proceedings - ISMB/ECCB 2011

Proceedings Chair: Mona Singh, Princeton University, USA
Proceedings Co-chair: Joel Bader, John Hopkins University School of Medicine, Baltimore, USA

**Call for Papers Submission Site** Opens October 19, 2009

ISMB 2010 will bring together Bioinformaticians and Computational Biologists working in a wide range of disciplines, including molecular biology, biology, medicine, computer science, mathematics and statistics. Papers that demonstrate both the development of new computational techniques AND their application to Molecular and Systems Biology, with significant outcomes to biomedical, agricultural, and environmental questions are especially encouraged.

We are soliciting high-quality research papers in any aspect of computational biology, including the following areas:

For a more complete listing of committee members click here

Relevant computational techniques include, but are not limited to: machine learning; data mining; text analysis; pattern recognition; knowledge representation; databases; data modeling; combinatorics; stochastic modeling; string and graph algorithms; linguistic methods; robotics; constraint satisfaction; data visualization; parallel computation; data integration; modelling and simulation.

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Papers will be assigned to an Area and three reviews sought. Accepted papers will be published as conference proceedings in an open access, online-only, section of a regular issue of the Bioinformatics journal with CDs distributed to conference delegates. Printed proceedings will be available for pre-order purchase during the online conference registration until May 28, 2010. The proceedings will be available online approximately one month prior to the conference opening.

Publication of the proceedings as an online part of the Bioinformatics journal will result in fully citable articles, indexed by Medline and ISI. See the conference proceedings of ISMB/ECCB 2007; ISMB 2008, ISMB/ECCB 2009 for an example of online-only publication by Oxford University Press.

Presenters of accepted papers will be given a 20-minute time slot (plus 5 minutes for questions) in the conference schedule to provide a summary and update to their work.

Papers can be submitted in either a template-free format or in the format following the template for author submission to the OUP journal bioinformatics. If the OUP template is used the paper length must not exceed nine pages. If the template-free format is used the length of the paper must not exceed 12 pages (single space, 12 point font), including abstract, figures, tables, and bibliography. In either case, the paper must contain an abstract whose length does not exceed 250 words.

After acceptance papers will have to be formatted according to the layout style required by the OUP bioinformatics journal and will be limited to 9 pages. Formatting requirements can be found at: http://www.oxfordjournals.org/bioinformatics/for_authors/submission_online.html

If absolutely necessary, submissions can be accompanied by supplementary material, similar to submissions to scientific journals. The supplementary material should be collected in a separate file that is appropriately marked and uploaded as an attachment on the paper submission page in EasyChair. However, we advise against adding supplementary material, in general. Supplementary material will be published on the proceedings site alongside the online version of the conference paper. We do not support supplementary material presented at any other than the publisher's site. Additionally, OUP does not edit or typeset supplementary data - it is uploaded online exactly as it is received, so authors must ensure its accuracy before submitting.

Papers should be submitted in their final form since the evaluation procedure does not allow for additional rounds of refinement / modification in response to referee criticisms. Poor quality submissions or insufficiently prepared papers are very often rejected.

PAPERS NOT CONFORMING TO THESE GUIDELINES WILL BE RETURNED WITHOUT REVIEW.

Papers will be accepted electronically after October 19, 2009 at the submission site in PDF format only.

Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to ISMB 2010, and for the entire review period, the paper should not be under review by any other conference or scientific journal.

The deadline for ISMB 2010 paper submissions is Friday, January 8, 2010. (You have until 11.59 p.m. in the time zone of your choice. This means that the submission server will be closed at noon, 11:59 am GMT (UTC+0), January 9, 2010).

Notification of conditional acceptance will be provided by e-mail no later than Monday, March 12, 2010. Final, corrected versions of accepted papers, which must conform to the formatting guidelines available when the paper is accepted, are due no later than March 26, 2010. Details of the submission process and format of accepted papers will be provided at the time of paper acceptance.

Papers not accepted may be resubmitted as a "regular conference poster" until April 2, 2010 or as a "late conference poster" until April 30, 2010. Poster information is available here.

For questions concerning the scientific content of submissions, please contact This email address is being protected from spambots. You need JavaScript enabled to view it..

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Technology Track

Technology Track submissions should be submitted via the online submission system here prior to April 23, 2010.

Technology Track Chair: Rodrigo Lopez, European Bioinformatics Institute, Cambridge, UK

The Technology Track allow organizations to showcase their software and/or hardware relevant to the bioinformatics / molecular biology community.
 

To conduct a Technology Track presentation, organizations must complete the on-line sign-up form including a brief description (50 words maximum) and a one (1) page Technology Track presentation overview (PDF).

The cost to present a Technology Track at ISMB 2010 is:
 

• For profit organization: US$2000.00
• Not for profit organization: US$400.00

Organizations receive:

• 50 minute presentation time allotted to for profit organizations or 25 minute presentation time allotted to non profit organizations (time and date scheduled by ISMB 2010)
• Listing in the conference program, including presentation time in the main schedule and a 50 word summary in the conference program book
• Listing on conference web site for overview of organizations Technology Track presentation
• Private Technology Track presentation room
• Audio-Visual equipment provided includes internet connection, data projector, screen, microphone (all additional equipment required will be charged at cost to the presenting organization)
• **Does not include conference registration** Presenters must be registered to attend ISMB in order to provide a presentation.

Format
Technology track presentations will be scheduled in either 25 or 50 minute time slots. Presenters must finish on time to allow for the set-up for the following presentation.

Presenters will be provided with a Windows-based desktop computer and Internet access. If a different operating system is required presenters should bring their own computer and contact the audiovisual team at least 24 hours before you are due to give your presentation.

If you intend to use a Windows computer provided by the conference for your Technology Track presentation, please bring a CD/Flash-drives containing any software and presentation material that needs to be loaded, or make your software and other material downloadable via the internet.

Within your time slot, you are at liberty to demonstrate your software in any way that you see fit: for example, you can combine one or more structured talks with live demos and question-and-answer sessions. Authors should provide handouts for attendees.

Major sponsors will be given precedence for Technology Track time slots.

Acceptance and Confirmation
All submissions will reviewed by the Technology Track selection committee and notification of acceptance will be forwarded no later than April 30, 2010. Technology Track presenters will be contacted by ISMB 2010 regarding presentation acceptance, Technology Track schedule, logistics and payment. Payment should not be made until organizations receive notification of acceptance.

For information on Technology Tracks contact This email address is being protected from spambots. You need JavaScript enabled to view it.

*** Click here to sign-up for an ISMB 2010 Technology Track ***

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CALL FOR POSTERS – ISMB 2010

Attention Poster Authors: When preparing your posters please note that your poster should not exceed the following dimensions: 46 inches wide by 45 inches high. There will be 2 posters per side on the each poster board. One poster will be an odd number and the other will be an even number. View a diagram of the the poster board in pdf format here.  

**Call for Posters Submission Site** Opens November 30, 2009

Poster Chair: Yana Bromberg, Columbia University, New York, USA

The organizers of ISMB 2010 invite all interested participants and conference attendees to consider presenting a poster.

ISMB 2010 will bring together scientists from a wide range of disciplines, including molecular biology, biology, medicine, computer science, mathematics and statistics. We are soliciting high-quality research posters in any aspect of computational biology.

Posters are intended to convey a scientific result and are not advertisements for commercial software packages. There will be a separate space for Industry Posters in the exhibition area. A poster that is judged by the conference organizers to be an advertisement will be subject to removal without notice.
Posters submitted to ISMB 2010 may cover any area of computational biology. We also encourage submission of purely experimental work and experimental posters should be submitted to the category (noted below) most accurately reflecting the area of this work and will be displayed accordingly. Posters must include original work that is unpublished or published after August 1, 2009.

Posters submitted for ISMB 2010 will be reviewed by the poster selection committee and notification of acceptance will be provided to the corresponding author by April 2, 2010.

Posters submitted by March 19, 2010 may be eligible to apply for ISMB 2010 Conference Travel Fellowships. Posters submitted as part of the late poster submission deadline are NOT eligible to apply for ISMB 2010 Conference Travel Fellowship Support.

All poster abstracts must be submitted using the conference submission site by the abstract deadline: Wednesday, March 19, 2010 (You have until 11.59 p.m. in the time zone of your choice). Space for posters is limited, and while we will make every effort to accommodate all interested groups, we advise you to submit your poster well before the deadline.

Submissions received after March 19, 2010 will be considered for the late poster acceptance. Posters submitted by the March 19, 2010 deadline will be notified of acceptance by Friday, April 2, 2010. You must submit two versions of your poster abstract: a 50-word abstract that will be printed in the conference program and a one-page abstract (~250 words/ PDF format) that will be posted on the conference web site. The abstract should not contain your title/position or any personal information (e.g. affiliation). There is a maximum of one poster per presenting author. The presenting author of a poster must be present at the conference and be available at the poster session to which their poster is assigned. Any author may submit to various conference tracks in addition to submitting a poster for review.

The poster dimensions will be posted by April 2, 2010. Fasteners (Velcro / double sided tape) will be provided at the site, please DO NOT bring tape, tacks or pins.

ISMB 2010 will not offer tables for laptop computer demos during the poster session. If you would like to demonstrate your software, you are encouraged to submit an application for Technology Track.

All abstracts will be considered a "personal communication" to the conference attendees. Abstracts will not be published in the proceedings, but will appear in the program and on the conference website.

Submitted posters will be reviewed and categorized into the following general areas:

• Microarrays
• Bioinformatics of Health and Disease
• Biophysics
• Chemical and Pharmaceutical Informatics
• Comparative Genomics
• Databases
• Evolution
• Functional Genomics
• Gene Prediction
• Genome annotation
• Genomics
• Institutional Research read more
• Interactions
• Machine Learning
• Neuroscience
• Ontologies
• Population Genetics and Variation
• Proteomics
• Regulation
• Reviews read more
• Sequence analysis
• Structure and Function Prediction
• Structural Genomics
• Systems Biology & Networks
• Text Mining
• Other: Posters that do not fall into the above categories may be considered as well.

All questions pertaining to the ISMB 2010 poster session should be directed to: This email address is being protected from spambots. You need JavaScript enabled to view it.

**Call for Posters Submission Site** Opens November 30, 2009

Public Institutions (Not for profit) are able to submit their research findings as part of the call for posters. This will be displayed with in the topic area of Institutional Research

Individuals may choose to submit a poster presenting a review of a specific field or technique. These submissions do not need to contain original work from the author and are intended to be an introduction for individuals not familiar with the field or technique. These review are not meant to be advertisements (e.g. it is not acceptable that the poster is an advertisement for a book or other type of commercial publication)

CALL FOR LATE POSTERS – ISMB 2010

Attention Poster Authors: When preparing your posters please note that your poster should not exceed the following dimensions: 46 inches wide by 45 inches high. There will be 2 posters per side on the each poster board. One poster will be an odd number and the other will be an even number. View a diagram of the the poster board in pdf format here.  

**Call for Posters Submission Site** Opens March 26, 2010

Poster Chair: Yana Bromberg, Columbia University, New York, USA

The organizers of ISMB 2010 invite all interested participants and conference attendees to consider presenting a poster as part of the Call for Late Posters.

ISMB 2010 will bring together scientists from a wide range of disciplines, including molecular biology, biology, medicine, computer science, mathematics and statistics. We are soliciting high-quality research posters in any aspect of computational biology.

Posters are intended to convey a scientific result and are not advertisements for commercial software packages. There will be a separate space for Industry Posters in the exhibition area. A poster that is judged by the conference organizers to be an advertisement will be subject to removal without notice.

Posters submitted to ISMB 2010 may cover any area of computational biology. We also encourage submission of purely experimental work and experimental posters should be submitted to the category (noted below) most accurately reflecting the area of this work and will be displayed accordingly. Posters must include original work that is unpublished or published after August 1, 2009.

Posters submitted during the ISMB 2010 Call for Late Posters will be reviewed by the poster selection committee and notification of acceptance will be provided to the corresponding author by May 14, 2010.

Posters submitted as part of the late poster submission deadline are NOT eligible to apply for ISMB 2010 Conference Travel Fellowship Support.

Late poster abstracts must be submitted using the conference submission site by the abstract deadline: Friday, April 30, 2010 (You have until 11.59 p.m. in the time zone of your choice). Space for posters is limited, and while we will make every effort to accommodate all interested groups, we advise you to submit your poster well before the deadline.

 You must submit two versions of your poster abstract: a 50-word abstract that will be printed in the conference program and a one-page abstract (~250 words/ PDF format) that will be posted on the conference web site. The abstract should not contain your title/position or any personal information (e.g. affiliation). There is a maximum of one poster per presenting author. The presenting author of a poster must be present at the conference and be available at the poster session to which their poster is assigned. Any author may submit to various conference tracks in addition to submitting a poster for review.

ISMB 2010 will not offer tables for laptop computer demos during the poster session. If you would like to demonstrate your software, you are encouraged to submit an application for Technology Track.

All abstracts will be considered a "personal communication" to the conference attendees. Abstracts will not be published in the proceedings, but will appear in the program and on the conference website.

Submitted posters will be reviewed and categorized into the following general areas:

• Microarrays
• Bioinformatics of Health and Disease
• Biophysics
• Chemical and Pharmaceutical Informatics
• Comparative Genomics
• Databases
• Evolution
• Functional Genomics
• Gene Prediction
• Genome annotation
• Genomics
• Institutional Research read more
• Interactions
• Machine Learning
• Neuroscience
• Ontologies
• Population Genetics and Variation
• Proteomics
• Regulation
• Reviews read more
• Sequence analysis
• Structure and Function Prediction
• Structural Genomics
• Systems Biology & Networks
• Text Mining
• Other: Posters that do not fall into the above categories may be considered as well.

All questions pertaining to the ISMB 2010 poster session should be directed to: This email address is being protected from spambots. You need JavaScript enabled to view it.

**Call for Posters Submission Site** Opens March 26, 2010

Public Institutions (Not for profit) are able to submit their research findings as part of the call for posters. This will be displayed with in the topic area of Institutional Research

Individuals may choose to submit a poster presenting a review of a specific field or technique. These submissions do not need to contain original work from the author and are intended to be an introduction for individuals not familiar with the field or technique. These review are not meant to be advertisements (e.g. it is not acceptable that the poster is an advertisement for a book or other type of commercial publication)

Call for Proposals: Special Interest Groups

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Call for ISMB  2010 Special Sessions Proposals

Special Session Chair: Michal Linial, The Hebrew University of Jerusalem, Israel

ISMB 2010 will feature a Special Sessions track that will run throughout the conference in parallel to other tracks (except the keynote presentations). In this setting, each Special Session resembles a mini-conference within the main ISMB meeting.

These Special Sessions have the purpose of introducing the ISMB/ECCB community to relevant 'hot' topics that were not covered in previous meetings. A wide range of topics are possible, as long as they importantly influence computational biology and bioinformatics. They might, for example, cover emerging themes that ISMB and ECCB are not currently approaching with the desired proficiency. We encourage you to submit a proposal on an area that in your eyes is important to the computational biology community and may impact the future of the field.

Special Sessions were introduced at ISMB/ECCB 2007 and since this time have become one of the most successful components of this conference.

This call is an invitation for scientists and professionals to submit proposals for special sessions for ISMB 2010, to take place in Boston, USA, between the dates of July 11 - 13.

Technical instructions:
Special sessions run the same schedule as all other parallel tracks. They must be designed as half-day sessions (2 hours) and synchronized with other tracks. The regular presentation unit is 30 minutes consisting of  20 minute talks + 5 minute discussion + 5 minutes for movement between parallel tracks. Sessions may include any form of presentation such as talks or panel discussions.

Preference will be given to emerging fields and to related fields in which the ISMB community needs to acquire higher proficiency. Special sessions are expected to provide a broad perspective on an emerging research field. Sessions will be selected from the submissions to this open call. Potential fields of interest include metabolomics, epigenetics and imaging. Additional topics of particular interest to the ISMB/ECCB community are welcome.

Proposals for special sessions should be submitted via the online submission system at http://www.iscb.org/submissions/specialsessions/ prior to October 16, 2009.

How to submit: Submissions must include a one-page description of the field, its relevance to the ISMB community, and the reasons for planning a session on this topic at ISMB 2010. Submitters may want to briefly describe their qualification to organize the Special Session. These explanations could be followed by a list of topics for possible presentations with one-paragraph descriptions. Finally, a draft of the time schedule for the session should be presented. A finalized list of speaker names is not necessary but may add weight to the proposal. If you list invited speakers as "accepted", please make sure that they agree to speak given to the financial constraints describe below.

Financial constraints: Special Sessions are an integral part of the ISMB meeting. Special Sessions chairs and speakers must pay their expenses including registration to the meeting. Therefore, the organizers highly encourage session organizers to seek independent funding, and to include any commitment that they may have secured in the proposal. ISMB will help in the administrative aspects of assigning the rooms, announcements and adding the detailed schedule to the conference program. Note that the ISMB cannot financially support the speakers or the Special Session organizers.

Submission evaluation: All submissions will be evaluated by a committee, which will consider the following criteria:

Call for Highlights Track Proposals

Highlights Track: About
Highlights Track: Deadlines
Highlights Track: Review Criteria
Highlights Track: Submission Guidelines

Highlights Track Submission Site - Opens October 26, 2009

Highlights Track Chair: Burkhard Rost, Columbia University, New York, USA

The Highlights Track was introduced at ISMB/ECCB 2007 in Vienna, and immediately ranked as one of the top three events in the popularity, behind Keynotes and Special Sessions. Since its introduction it continues to be one of the most popular conference tracks.

We invite the submission of full papers that have been published, or accepted for publication, between January 1, 2009 and the submission deadline (February 26, 2010) Publications that are "in press" and already linked on the journal web site are also welcome. A group of experts will select the papers to be presented at the meeting considering the impact of the work on the field, the likelihood that the work will make a good presentation, and the relevance to biomedical research, in general. Accepted presenters for the Highlights Track are required to make the presentation themselves, and must register and pay to attend the conference.

Submissions should include a 250-word abstract-like argument that explains how the work of the submitted paper(s) is impacting the field. More details are given below.

All submissions will be evaluated by a group of editors. Upon submission, the authors will identify the editor/expert most suitable to suitable to review their work.

All papers published in peer-review journals (no book chapters) between January 2009 and February 26, 2010 are eligible to be presented as talks. Papers in press are acceptable only if already available through the journal web site. Note that presenters are be encouraged to also present more recent work, however, that work will not be considered in the decision. Up to 2 papers can be submitted as one single PDF if the authors intend to present the results of multiple qualifying papers.

PDF files of the papers and the 250-word support abstract can only be submitted through the automated system by February 26, 2010 (midnight by any time zone). No exceptions will be allowed.

The editors will notify authors of the acceptance by Friday, March 26, 2010.

The selected Highlights will be presented in tracks that run in parallel to the main ISMB meeting, July 11-13, 2010. All presentations will have to be completed within 20 minutes and will be followed by 5-minute discussions. While presenters are expected to focus most ly on the chosen paper(s), short infusions of more recent results are welcome.

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All submissions will be evaluated by a group of editors to be named, and judged according to the following criteria:

1. Relevance, interest, and value of the topic to ISMB attendees,
2. Impact of the paper(s) on biology/medicine (while the impact of papers on science is not fully reflected by ISI/Google-like impact factors or high number of downloads, high values in such factors will clearly stand as a strong argument for acceptance),
3. "Presentability" of the work to a large, diverse audience,
4. Quality of oral presentations by the submitter (if known),
5. Submissions that permit the presentation of related interesting unpublished new results will be viewed favorably.

These "soft" criteria attempt to capture the underlying goal of the Highlights Track, namely the presentation of exciting and thought-provoking seminars that will both contribute to the success of ISMB and to the impact the meeting has on advancing computational biology and bioinformatics.

PDF files of the papers and the 250-word support abstract can only be submitted through the automated system by February 26, 2010 (midnight by any time zone). No exceptions will be allowed.

Submissions must be made to the automatic Highlights Track Submissions Site.
Submissions should include the following:

• Name/affiliation/email of submitter (assumed to be the presenter; note that the presenter cannot be changed because the identity and ability to present of that person will be an essential selection criterion).
• Names/affiliations/email of ALL coauthors (note: any name appearing on a published paper has to be added here). Note that all co-authors have to agree to the submission. It is the responsibility of the submitter to guarantee that all co-author email addresses are correct (email notifications of the submission will be sent to all co-authors).
• 150  word description of the presentation for promotion on conference website.
• Additional contact information (for presenter).
• 250-word limited abstract-like argument that explains the impact and importance of this work.
• Sources of original publication(s) (Year, Journal, Vol., pages).
• PDF with paper(s) (note: in case of the submission of 2 papers, both should be merged into one single PDF; all reviews will be based on the content of this PDF).
• Optional: link to Google Video demonstrating presentation skills of presenter.
• Only PDF submissions are acceptable. The submission system is currently unable to handle ASCII, Word, LaTeX, or anything other than standard PDF. It is the responsibility of the submitter to verify that the PDF is completely viewable/printable by all major operating systems (LINUX, MacOS, Windows).
• Each presenter can submit a maximum of one application to present a highlight. The maximal number of submissions per author/co-author is 5.
All questions pertaining to the Highlights Track should be directed to:

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