Call for Highlights - ISMB/ECCB 2015

Highlights Track Chairs: Burkhard Rost, Technical University Munich, Germany, and,
                                              Reinhard Schneider, University of Luxembourg

Highlights Track Submission Site - Closed: February 27, 2015

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

We invite the submission of full papers that have been published, or accepted for publication, between January 1, 2014 and the submission deadline, February 27, 2015. Publications that are "in press" and already linked on the journal web site by February 27, 2015 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 Scientific Justification (abstract-like argument) that explains how the work of the submitted paper(s) is impacting the field. More details are given below.

New for 2015 will be the presentation of talks by Thematic area. Oral presentations from accepted submissions from Highlights, Proceedings and Late Breaking Research will be presented by theme area. These themes are:

Genes:
Includes work in genes (including non-coding RNA), transcriptomes, genomes and variation.

Proteins:
Includes analysis of proteins and their structures and proteomics.

Systems:
This theme includes higher level systems such as cells, tissues, whole organisms and ecosystems. Includes systems biology, molecular interactions and genetic regulation.

Disease:
Includes analysis of mutations, phenotypes, drugs, epidemiology and other clinically relevant areas

Data:
Includes data and text-mining, ontologies, databases and machine learning approaches that do not fit in other categories.

Other:
Research areas that do not fall within the five (5) main thematic areas. The organizers may, at their discretion, move submissions to other thematic areas.
 

All papers published in peer-reviewed journals (no book chapters) between January 1, 2014 and February 27, 2015 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.

Acceptance notifications will be sent no later than Friday, April 10, 2015.  **Revised**

The selected Highlights will be presented in tracks that run in parallel at the conference. All presentations should be no longer than 15 minutes and will be followed by a maximum of 3-minute discussions.  Presenters should focus on the chosen paper(s), and are encouraged to include more recent results. In fact, closed stories that conclude with a particular publication not bearing follow up perspectives might not constitute the best Highlight presentations.
 

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All submissions will be evaluated by a group of Area Chairs and the submission will be evaluated according to the following criteria:

1. Relevance, interest, and value of the topic to conference 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 the conference and to the impact the meeting has on advancing computational biology and bioinformatics.

PDF files of the papers,  the 250-word Scientific Justification (support abstract) and a 150-word presentation description must be submitted through the automated system by February 27, 2015 (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:

• For each presenter only one submission to the Highlights Track will be reviewed (the LAST will be taken by default). The same limitation applies for the last author (group). Publications can be grouped if it becomes clear how different publications will be combined in a talk. The maximal number of submissions per author/co-author is 5.
• 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).

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

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Call for Late Breaking Research Track Proposals - ISMB/ECCB 2015

Late Breaking Research Track Submissions - Closed: March 27, 2015

ISMB/ECCB 2015 brings together Bioinformaticians and Computational Biologists working in a wide range of disciplines, including molecular biology, biology, medicine, computer science, mathematics and statistics. The LBR Track provides authors an opportunity to submit late breaking research to ISMB delegates. 

New for 2015 will be the presentation of talks by Thematic area. Oral presentations from accepted submissions from Highlights, Proceedings and Late Breaking Research will be presented by theme area. These themes are:

Genes:
Includes work in genes (including non-coding RNA), transcriptomes, genomes and variation.

Proteins:
Includes analysis of proteins and their structures and proteomics.

Systems:
This theme includes higher level systems such as cells, tissues, whole organisms and ecosystems. Includes systems biology, molecular interactions and genetic regulation.

Disease:
Includes analysis of mutations, phenotypes, drugs, epidemiology and other clinically relevant areas

Data:
Includes data and text-mining, ontologies, databases and machine learning approaches that do not fit in other categories.

Other:
Research areas that do not fall within the five (5) main thematic areas. The organizers may, at their discretion, move submissions to other thematic areas.

All presentations should be no longer than 15 minutes and will be followed by a maximum of 3-minute discussions.

Submissions and evaluation criteria:

Authors are to provide a 2 page, total, extended abstract of their work, including one (1) figure (11pt font, 1.5-inch margins). References can be included in the two pages. Submitters may choose to provide a link to a short (<=5min) video (eg. youtube) of them presenting their work, to assess presentation skills. Submissions will also be evaluated on the potential for an excellent and interesting presentation. Significance, interest to the bioinformatics community, and biological/medical impact would be the key evaluation criteria. Each submitter must provide a title, a short one (1) paragraph public abstract for inclusion in the electronic conference program and website. A one or two (1 or 2) sentence summary of novelty and significance of the work is to be included. During the submission process you will be able to confirm if your work will also to be presented as a poster.

For more information please contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

Call for Proceedings - ISMB/ECCB 2015

This email address is being protected from spambots. You need JavaScript enabled to view it.: Yves Moreau, Ku Leuven, Belgium, and
                                              Niko Beerenwinkel, ETH Zurich, Basel, Switzerland

Call for Proceedings Submission Site: https://easychair.org/conferences/?conf=ismbeccb2015   --  Closed

ISMB/ECCB 2015 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.

Review  Process:

Submissions will be subject to two rounds of reviews, allowing the authors to reply to the reviewer comments. In the first round the submissions will be classified into three categories: (a) accept/minor changes, (b) major changes, and (c) not accepted.  Papers in the first category will be accepted without a second round of review. Authors of submissions in the second category will be given the opportunity to submit revised drafts based on the reviewer comments, with letters of reply to the reviewers outlining the main changes and/or giving counter arguments to the reviewer points. We expect the majority of papers to fall in categories (a) and (c), with category (b) reserved for papers that the reviewers identified as strong but with substantial issues that need to be addressed. Among the resubmitted papers, the second round of review will select the most suitable papers for presentation. These will be published in the Bioinformatics journal and presented at the conference. The authors of submissions that will not be accepted in the second round will be given the opportunity to be redirected to an on-line issue of the Bioinformatics journal (fully citable; equal to regular publication in this journal), subjected to the Editorial considerations of Bioinformatics.

New for 2015 will be the presentation of talks by Thematic area. Oral presentations from accepted submissions from Highlights, Proceedings and Late Breaking Research will be presented by theme area. These themes are:

Genes:

• Gene Regulation & Transcriptomics
• Evolution and Comparative Genomics
• RNA Bioinformatics
• Sequence Analysis

Includes work in genes (including non-coding RNA), transcriptomes, genomes and variation.

Proteins:

• Mass Spectrometry & Proteomics
• Protein Interact & Molecular Networks
• Protein Structure & Function

Includes analysis of proteins and their structures and proteomics.

Systems:

• Metabolic Networks
• Population Genomics

This theme includes higher level systems such as cells, tissues, whole organisms and ecosystems. Includes systems biology, molecular interactions and genetic regulation.

Disease:

• Disease Models & Epidemiology

Includes analysis of mutations, phenotypes, drugs, epidemiology and other clinically relevant areas.

Data:

• Databases, Ontologies, & Text Mining
• Bioimaging & Data Visualization
• Applied Bioinformatics

Includes data and text-mining, ontologies, databases and machine learning approaches that do not fit in other categories.

Other:
Research areas that do not fall within the five (5) main thematic areas. The organizers may, at their discretion, move submissions to other thematic areas.

Submitters will choose the track area best suited to their paper during the submission process. The Area Chairs will be announced shortly.

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 Track Areas and three reviews sought. Papers may be moved between areas as appropriate - this is often necessary for load balance and fit between areas during the review process. Accepted papers will be published as conference proceedings in an open access, online-only, section of a regular issue of the Bioinformatics journal with an electronic version distributed to conference delegates. 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 for ISMB/ECCB 2013 for an example of online-only publication by Oxford University Press.

ISMB/ECCB 2015 provide authors of accepted papers an oral presentation to provide an oral summary of their work. All presentations should be no longer than 15 minutes and will be followed by a maximum of 3-minute discussions

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. Paper presenters must register and pay to attend and present at the conference.

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

Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to ISMB/ECCB 2015, and for the entire review period, the paper should not be under review by any other conference or scientific journal.

Papers will be accepted electronically, in PDF format only, at the submission site until Friday, January 16, 2015 (midnight any time zone).

Notification of submissions selected for second rounds will be notified by February, 13, 2015. The revised submission deadline for these second round papers will be March 13, 2015. Conditional acceptance will be provided by e-mail no later than April 6, 2015. Final, corrected versions of accepted papers, which must conform to the formatting guidelines available when the paper is accepted, are due no later than April 10, 2015 and Final acceptance notification is April 17, 2015. Details of the submission process and format of accepted papers will be provided at the time of paper acceptance.

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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Call for Special Sessions Proposals - ISMB/ECCB 2015

Special Session Chair: This email address is being protected from spambots. You need JavaScript enabled to view it., The Hebrew University of Jerusalem, Israel

** Special Sessions Submissions - Closes: December 5, 2014

ISMB/ECCB 2015 will feature a Special Sessions track (SST) that will run throughout the conference in parallel to other tracks (except the keynote presentations). In its structure, each Special Session provides more in-depth look at the subject matter presented. Proposals for special sessions should be submitted via the online submission system at here by December 5, 2014.  In case you would like to consult on your proposed idea prior to submission please contact Michal Linial (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Special Sessions have the purpose of introducing the ISMB/ECCB community to relevant 'hot' topics that were not covered in previous meetings or that had gone through fast evolution in recent years.  It can be considered as a mini-symposium on a frontier of timely topic, presented by top experts. 

A wide range of topics is possible, as long as they importantly influence computational biology and bioinformatics. We also encourage topics that are marginal to computational biology but clearly will need the involvement of such expertise in the near future. The proposed topics for SST  might, for example, cover emerging themes that ISMB/ECCB is not currently approaching with the desired proficiency. Some attractive topics include "Analysis on a single molecule level"; "A computational view of 3D-chromatin "; "Optogenetics – live imaging of the brain"; "the Microbiome and Virome"; “Ancient DNA-human evolution” etc.

In addition we would like to encourage submission that deal with the Society-Computational Biology interface including open issues. Examples might be “Stem cells and ethics”; “Matrices for success and impact” etc. We encourage you to submit a proposal on an area that you deem as important to the computational biology community and may impact the future of the field.

This call is an invitation for scientists and professionals to submit proposals for special sessions for ISMB/ECCB 2015, to take place in Dublin, Ireland, July 12 - 14.

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/ECCB 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 here prior to December 5, 2014.
 

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/ECCB 2015. 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.

Special Sessions are an integral part of the ISMB/ECCB meeting. Special Sessions chairs and speakers MUST pay their expenses 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 coordinate the administrative aspects of room assignments, announcements and adding the detailed schedule to the conference program. Note that the ISMB/ECCB cannot financially support the speakers or the Special Session organizers.
 

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