Submission Deadline Approaching: RECOMB Satellite Conference on Regulatory and Systems Genomics, with DREAM Challenges

Dear ISCB Members and Colleagues,

The deadline for submissions for the 5th annual joint RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, is just two weeks away. We invite you to participate by submitting a paper or abstract.

For more information, visit: http://recomb-2012.c2b2.columbia.edu/.

The 5th annual joint RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges is one of the premier annual meetings for computational and experimental scientists in the fields of regulatory genomics and systems biology, and is now an official conference of the International Society for Computational Biology. The meeting will be held at the Hotel Sofitel San Francisco Bay on November 12-15, 2012.

All submissions of full-length papers will be considered for publication in Genome Research and the Journal of Computational Biology. Accepted papers will be published in conjunction with the conference and authors of selected papers will present their work at the meeting. Our program committee will review all submitted papers in collaboration with the journal editors and the conference chairs.

We are also accepting submissions of abstracts, including both original unpublished work and work that has been published or accepted for publication by a high-impact journal between January 1 and November 1, 2012. Unpublished work will be considered for either an oral or a poster presentation. Work already accepted for publication will be considered for an oral presentation only.

***The deadline for all submissions is September 7, 2012 ***

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation. Areas of interest for papers, abstracts, and nominations include:

• Modeling and recognition of regulatory motifs and modules
  
• Chromatin state establishment, maintenance, and role in development
• Post-transcriptional regulation and small regulatory RNAs
• Regulatory networks, metabolic networks, proteomic networks
• Cellular signatures of biological responses and disease states
• Phosphorylation, metabolic fluxes, systematic phenotyping
• Mathematical modeling and simulation of biological systems
• Methods for systematic validation of high-throughput biological predictions
• Approaches for aggregation of results arising from different methodologies

We are also still accepting submissions for participation in the DREAM Challenges, designed to identify the best practices for predicting the structure of biological networks. Lastly, we are also still inviting nominations for RegGen-TopTen 2011, our list of the most influential papers of 2011 in the fields of Regulatory and Systems Genomics, in conjunction with the ISMB Special Interest Group on Regulatory Genomics (RegGen SIG). See our website above for more information.

We are looking forward to very exciting program. Our invited speakers include Howard Chang, Job Dekker, Angela DePace, Joe Ecker, Yoav Gilad, Len Pennacchio, Saurabh Sinha, Stephen Friend, Jonathan Weissman, Dean Felsher, Michael Elowitz, Joe Nadeau, Markus Covert, Joe Gray, and Ernest Fraenkel.

We hope that you will participate and look forward to seeing you in San Francisco this November!

Best regards,

Andrea Califano, Manolis Kellis, Sylvia Plevritis, and Gustavo Stolovitzky

Conference Chairs

Call for Highlights Papers and Posters:  ISCB-Asia/SCCG 2012

ISCB-Asia/SCCG 2012, co-hosted by ISCB and BGI, will be held in Shenzhen, China from December 17-19. Confirmed keynote speakers include Gunnar von Heijne, Philip Greene, Piero Carninci, Takashi Ito, Eric Xing and Zhiping Weng. They will be joined by several prominent invited speakers in special sessions including: computational tools for NGS, cancer informatics, and cloud and work flows for reproducible biology. ISCB is known for hosting a variety of international meetings including ISMB, while BGI of Shenzhen is one of the world's largest sequencing centers. Shenzhen is a booming city with easy access from adjacent Hong Kong and a pleasant climate during December.

Call for Highlights: We invite the submission of talks describing research published as full journal papers between August 31, 2011 and September 30, 2012 of topics including, but not limited to: computational tools for NGS, cancer genome informatics, cloud and work flows for reproducible bioinformatics, protein bioinformatics, metagenomics, RNA informatics, machine learning, and open problems in computational biology. Publications that are "in press" and already linked on the journal web site by September 30, 2012 are 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 biomedicine and computational biology. Accepted presenters to the Highlights Track are required to make the presentation themselves (rather than assign a co-author to make the presentation), 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.

Please note the following dates:

• Papers published from Aug 31, 2011 to Sep 30, 2012 considered.
• Submission deadline: Sep 30, 2012
• Notification Date: Oct 29, 2012

Please submit your Highlights papers directly to the ISCB submission site at www.iscb.org/submissions/index.php?id=128

Call for Posters: Poster abstracts in the same topic areas are also invited. Please submit your poster directly to the ISCB submission site at www.iscb.org/submissions/index.php?id=129 by the submission deadline of October 31, 2012. Accepted poster presenters must register and pay to attend the conference.

We look forward to receiving your submissions,

Victor Jin, The Ohio State University - Program Committee Chair

Paul Horton, AIST Japan - Conference Chair and Program Committee Co-Chair

CALL FOR PAPERS, ABSTRACTS, and NOMINATIONS - RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges

Dear colleague,

We are still accepting submissions of papers and abstracts for the 5th annual joint RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, which is now an official conference of the International Society for Computational Biology, and one of the premier annual meetings for computational and experimental scientists in the fields of regulatory genomics and systems biology. The meeting will be held at the Hotel Sofitel San Francisco Bay on November 12-15, 2012.

*** The deadline for all submissions is September 7, 2012. ***

Submission information is available at http://recomb-2012.c2b2.columbia.edu/.

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation.

Invited speakers include: Howard Chang, Job Dekker, Angela DePace, Joe Ecker, Yoav Gilad, Len Pennacchio, Saurabh Sinha, Stephen Friend, Jonathan Weissman, Dean Felsher, Michael Elowitz, Joe Nadeau, Markus Covert, Joe Gray, and Ernest Fraenkel.

We are now accepting submissions of full-length papers to be considered for publication in Genome Research and the Journal of Computational Biology. Accepted papers will be published in conjunction with the conference and authors of selected papers will be invited to present their work at the meeting. Our program committee will review all submitted papers in collaboration with the journal editors and the conference chairs.

We are also accepting submissions of abstracts, including both original unpublished work and work that has been published or accepted for publication by a high-impact journal between January 1 and November 1, 2012. Unpublished work will be considered for either an oral or a poster presentation. Work already accepted for publication will be considered for an oral presentation only.

Lastly, we are also excited to announce that we invite nominations for RegGen-TopTen 2011, our list of the most influential papers of 2011 in the fields of Regulatory and Systems Genomics, in conjunction with the ISMB Special Interest Group on Regulatory Genomics (RegGen SIG). First and last authors of these papers will be honored at the meeting and highlighted online. All nominations will be evaluated by leaders in the field, including our past keynote speakers.

Areas of interest for papers, abstracts, and nominations include:

• Modeling and recognition of regulatory motifs and modules
• Chromatin state establishment, maintenance, and role in development
• Post-transcriptional regulation and small regulatory RNAs
• Regulatory networks, metabolic networks, proteomic networks
• Cellular signatures of biological responses and disease states
• Phosphorylation, metabolic fluxes, systematic phenotyping
• Mathematical modeling and simulation of biological systems
• Methods for systematic validation of high-throughput biological predictions
• Approaches for aggregation of results arising from different methodologies

We are also still accepting submissions for participation in the DREAM Challenges, designed to identify the best practices for predicting the structure of biological networks.

We hope that you will participate and look forward to seeing you in San Francisco this November!

Best regards,
Andrea Califano, Manolis Kellis, Sylvia Plevritis, and Gustavo Stolovitzky
Conference Chairs

ROCKY CALL FOR ABSTRACTS AND EARLY REGISTRATION ARE NOW OPEN

December 6 - 8 , 2012, Snowmass/Aspen, Colorado, USA

Dear ISCB Members and Colleagues,

Please join us for the 10th Annual Rocky Mountain Bioinformatics Conference! The Rocky conference series has grown from a small regional event into an international program with a spotlight on regional development in the computational biosciences. Invited and accepted presenters represent a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world. The meeting is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

CALL FOR ABSTRACTS: The Rocky 2012 Conference (www.iscb.org/rocky2012) provides opportunities for short flash presentations (10 minute talks) on current projects from as many attendees as possible. Original presentations (including significant works-in-progress) are solicited in all areas that involve the application of advanced computational methods to significant problems in biology or medicine.

Submitters are given the option to apply for a 10-minute "flash" oral presentation, a poster presentation, or both. We will attempt to accommodate all requests from authors accepted for presentation. The submission form is located here: www.iscb.org/rocky2012-program/rocky2012-call-for-presentations.

Submission Form Key Dates:

• Submission Deadline: October 4, 2012
• Acceptance Notification: November 2, 2012

EARLY REGISTRATION IS OPEN: Take advantage of early registration rates by visiting: www.iscb.org/rocky2012-register. Please note that accepted presenters must register as a conference attendee by November 6 in order to give a presentation at Rocky 2012.

We look forward to your participation! Please feel free to share this invitation with your colleagues and collaborators - the Rocky conference offers a special Academic Retreat package for groups attending from the same lab or school, including a free student registration.

We hope to see you there!

The Rocky 2012 Conference Organizing Team

Last Call for Proposals to Organize ISCB-Asia 2013

Dear ISCB Members and Colleagues,

As a final reminder, ISCB is seeking proposals from individuals or groups interested in hosting the next open ISCB-Asia conference, slated for the third quarter of 2013, to co-organize this meeting with ISCB anywhere in the Asia region. Without exception the proposal deadline is the 1st of August, 2012. If you are not personally interested but know of someone else who could do an excellent job of organizing this event, please feel free to forward this mail. An overview of ISCB, its expansion into regionally-based international meetings, and the details of the proposal requirements are all specified below.

ISCB-Asia 2013 Meeting

The aim of the International Society for Computational Biology (ISCB) is to serve the worldwide computational biology community by addressing scientific policies, providing access to high quality publications, organising meetings, and serving as a portal to information about training, education, employment and news from related fields. ISCB currently has over 3000 members from more than 70 countries around the world. Among its many activities ISCB hosts annual meetings, including ISMB, the world's longest running and largest international bioinformatics conference (held jointly with ECCB every other year in Europe), as well as a series of smaller, newer meetings. ISCB also has affiliations in place with several other significant meetings in the field, such as PSB and RECOMB.

In an extension to its meeting activities, ISCB is participating in the organization of regional meetings in locations where ISMB has not been held. In 2009 and 2011 joint ISCB-Africa meetings were held in collaboration with the African Society for Bioinformatics and Computational Biology (ASBCB), and the 2013 meeting is now being planned for Tunis, Tunisia; in 2010 and 2012 ISCB-Latin America was held in Uruguay and Chile, respectively; the first ISCB-Asia was held jointly with InCoB 2011 in Malaysia, and the 2012 meeting is now being planned for China (Shenzhen). With the aim of continuing these successful regional meetings, ISCB is now soliciting applications for the co-organization of our next meeting in Asia for 2013.

A requirement that ISCB-Asia become permanently affiliated to an existing meeting or society is not intended. Having co-organised the ISCB-Asia meeting with the Asia-Pacific Bioinformatics Network in 2011 and with BGI in 2012, ISCB now looks to continue expanding its network of affiliations by seeking proposals from other existing societies or conferences in the Asia region, or by working with a group that has a similar interest in organising a new bioinformatics community meeting in Asia.

Preliminary proposals should provide (all of this information is also available as a PDF download):

• Names and short CVs of local organising committee members and their proposed roles
• Evidence of previous experience in organising mid- to large-sized meetings
• Planned meeting dates and location
• Budget proposal including basic costs (venue rental, speaker travel, etc.) and preliminary commitments for financial support from sponsors.
• Estimated meeting size
• Focus of scientific program (required if a focus on a specialist research topic is planned)
• Plans for publishing or online dissemination of the proceedings
• Evidence of co-operation among multiple groups within the Asian region

ISCB will:

• Participate through elected ISCB scientific representatives on the organising committee
• Endorse and advertise the meeting through its extensive mailing lists
• Suggest keynote speakers
• Potentially provide funds to seed the meeting (funds repayable to ISCB from conference proceeds)
• Provide budget guidance
• Potentially provide travel funds to support student participation

Criteria for evaluation

• Proposals that emphasize and encourage attendance from a diverse range of regional groups and attendees will have an advantage
• The meeting should be in a place where there is expected to be a sizeable local community from which attendance can be expected, as well as reasonable international access to a nearby airport
• Budget is within the range which can be covered by reasonably estimated registration fees alone, in the event that sponsor funding does not materialize
• Preference will be given to organising committees with diverse representation
• Proposers should have experience with organising meetings

Proposals should be submitted via email to This email address is being protected from spambots. You need JavaScript enabled to view it. by 1 August 2012.

Thank you,
Paul Horton, Chair, ISCB Conferences Committee
Janet Kelso, Co-Chair, ISCB Conferences Committee

Final Call for ISCB-Asia/SCCG 2012 Papers

Final Call for Papers - NOW CLOSED
Paper submission deadline: 30 July 2012

Call for Highlights
Highlights submission deadline: 30 September 2012

Call for Posters
Posters submission deadline: 31 October 2012

ISCB-Asia/SCCG 2012, co-hosted by ISCB and BGI, will be held in Shenzhen, China from December 17-19. Confirmed keynote speakers include Gunnar von Heijne, Philip Greene, Piero Carninci, Takashi Ito, Eric Xing and Zhiping Weng. They will be joined by several prominent invited speakers in special sessions including: computational tools for NGS, cancer informatics, and cloud and work flows for reproducible biology. ISCB is known for hosting a variety of international meetings including ISMB, while BGI of Shenzhen is one of the world's largest sequencing centers. Shenzhen is a booming city with easy access from adjacent Hong Kong and a pleasant climate during December.

We cordially invite you to submit original research in any area of computational biology as a Paper or Poster, and recently published research as a Highlights. Topics areas may include, but are not limited to: computational tools for NGS, cancer genome informatics, cloud and work flows for reproducible bioinformatics, protein bioinformatics, metagenomics, RNA informatics, machine learning, and open problems in computational biology.

There are several opportunities to submit your best research, with the first deadline coming in just one week (please note that submission deadlines are firm and cannot be extended for any reasons so please submit well before the deadlines):

Original Research Paper - Submission now CLOSED

Original research papers are highly encouraged. Please submit your papers directly to the ISCB submission site at www.iscb.org/submissions/index.php?id=124. Manuscripts should be in pdf format using a minimum of 10pt font at a maximum of 10 pages, including abstract, images/figures, and references (page margins must be at least 6mm or .5 inch). Accepted proceedings papers will be submitted to a special issue of BMC Bioinformatics/BMC Genomics or recommended for publication in Omics, or Gigascience. Submission of relevant review or trends in technology papers is also encouraged and will be considered for publication in a special issue of Briefings in Bioinformatics.
 

Highlights Paper - deadline is 30 September 2012

Papers published within the last 12 months or papers that are in press are acceptable only if already available through the journal web site. Note that accepted presenters are encouraged to also discuss 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. Please submit your Highlights papers directly to the ISCB submission site at www.iscb.org/submissions/index.php?id=128.

Poster - deadline is 31 October 2012

All poster abstracts to be included in the conference program must be submitted using the conference submission site by the abstract deadline. 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. Please submit your poster directly to the ISCB submission site at www.iscb.org/submissions/index.php?id=129.

Some of the details in this mail differ than previous notices about submission opportunities and dates from previous notices. Please refer to these dates as the final submission dates, and note that requests to accept late submissions for any reason cannot be considered.

We look forward to receiving your submissions and welcoming you to Shenzhen in December!

Sincerely,

Victor Jin, The Ohio State University - Program Committee Chair

Paul Horton, AIST Japan - Conference Chair and Program Committee Co-Chair

Final 48 Hours of ISCB Elections

Dear ISCB Member,

Just 48 hours remain for voting in the ISCB Officers and Student Council Leaders election. You can have a voice in determining the future of ISCB by participating in these elections. The positions being voted this year are:

• ISCB Vice President, ISCB Treasurer, and ISCB Secretary
  
• Student Council Rep to the ISCB Board of Directors, Student Council Chair, Student Council Vice-Chair, Student Council Secretary, and Student Council Treasurer

Please go to www.iscb.org/elections now to read the candidate statements and cast your ballot. (Logging in to your membership account is required to verify your membership status, but your ballot is 100% anonymous.)

Voting will close on July 25th and the new leaders will be announced as soon as possible following ratification of the results by the ISCB Board of Directors and the Student Council Leaders in August.

Thank you for your participation!
The ISCB Nominations & Elections Committee

FOR IMMEDIATE RELEASE

The International Society for Computational Biology Announces a Wikipedia Computational Biology Article Competition

July 15, 2012 - Long Beach, CA - At the 20th annual international conference on Intelligent Systems for Molecular Biology (ISMB), the president of the International Society for Computational Biology (ISCB), Burkhard Rost, together with Alex Bateman, senior investigator of the Wellcome Trust Sanger Institute, will announce on Sunday, July 15th, a competition to improve the existing Wikipedia articles about any aspect of computational biology.

A key component of the ISCB's mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at large. Wikipedia has become an important way to communicate all types of science to the public. The ISCB aims to further its mission by increasing the quality of Wikipedia articles about computational biology, and by improving accessibility to this information via Wikipedia. This extends the work of PLoS Computational Biology (an official journal of the ISCB), which links with Wikipedia to provide Education Track articles.

By introducing a competition during ISMB, the ISCB will capitalize on the depth of expertise among its members in attendance at ISMB, and through its community of members and colleagues around the world to support the Computational Biology WikiProject (en.wikipedia.org/wiki/Wikipedia:WikiProject_Computational_Biology). As Wikipedia is a collaborative endeavor, the competition will be open to both individuals and groups, and prizes will be awarded for best contributions.

About ISCB

The International Society for Computational Biology is a not-for-profit scholarly society based in La Jolla, California, at the San Diego Supercomputer Center on the campus of the University of California, San Diego. The ISCB has a global membership of nearly 3,000 researchers from 70 countries. For more information, visit www.iscb.org.

Press Contact
BJ Morrison McKay
ISCB Executive Officer
+1-760-522-8805
This email address is being protected from spambots. You need JavaScript enabled to view it.

20 Years ISMB - 15 Years ISCB (ISCB Newsletter - Summer 2012)

Dear Members and Colleagues,

We are pleased to submit to you our annual ISMB Focus Issue newsletter, which includes features on some of the most important ISCB activities and initiatives of this past year.

You are invited to access the full newsletter online at www.iscb.org/images/stories/newsletter/newsletter15-1/index.html

Or, you may prefer to download the PDF newsletter at www.iscb.org/images/stories/newsletter/newsletter15-1/ISCB-newsletter-15-1.pdf

As a preview, the Table of Contents for this newsletter includes the following articles:

• A Letter to ISCB Members & Colleagues (from President Burkhard Rost and Executive Officer BJ Morrison McKay)
• Officer and Student Council Elections (please note the elections closing date has changed since this was written: now July 25th)
• Spotlight on ECCB12
• Meet the ISCB Fellows Class of 2012
• Student Council Symposium Highlights
• Overton Prize: Ziv Bar-Joseph
• 2012 ISCB Sr. Scientist Award: Gunnar von Heijne
• Announcing ISMB/ECCB 2013 Berlin
• News from ISCB Student Council
• FASEB Updates
• Introducing Stacy Slagor
• PLoS Computational Biology Overview
• A Report of the Curriculum Task Force
• Bioinformatics Journal Update
• NIGMS Celebrates 50 Years
• ISCB Continues to Advocate for Open Access
• GLBIO 2012 Highlights
• Call for Proposals to Organize ISCB-Asia 2013
• ISCB Community Conferences & x-Meetings
• Upcoming Conferences & Events

Happy reading to you!

Sincerely,

BJ Morrison McKay, ISCB Executive Officer

CALL FOR PAPERS – RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges

Dear Colleague,

It is our pleasure to announce the 5th annual RECOMB Conference on Regulatory and Systems Genomics, with DREAM Challenges, one of the premier annual meetings for computational and experimental scientists in the fields of regulatory genomics and systems biology. This year the meeting has become an official conference of the International Society for Computational Biology, and will be held at the Hotel Sofitel San Francisco Bay November 12-15, 2012. As in the past, this year's meeting combines the following conferences:

• 9th Annual RECOMB Satellite on Regulatory Genomics
• 8th Annual RECOMB Satellite on Systems Biology
• 7th Annual DREAM Reverse Engineering Challenges

We are now accepting submissions of full-length papers to be featured and published in conjunction with the conference. Authors of selected papers will be invited to present their work at the meeting. In addition, we have arranged partnerships with the journals Genome Research and the Journal of Computational Biology to publish high-quality papers. Our program committee will review all submitted papers in collaboration with the journal editors.

We invite you to take advantage of this unique opportunity. Please use the EasyChair system to submit your manuscript at http://www.easychair.org/conferences/?conf=recombsbrgdream2012. Instructions on manuscript submission, as well as information about the program committee who will review papers is also available on the conference website at http://recomb-2012.c2b2.columbia.edu.

***The deadline for submissions is Friday, September 7. ***

This conference is designed to present the latest findings about regulatory and systems genomics, foster discussion about current research directions, and establish new collaborations that will advance the development of a systems-level understanding of gene regulation. Some possible topics include:

• Modeling and recognition of regulatory motifs and modules
• Chromatin state establishment, maintenance, and role in development
• Post-transcriptional regulation and small regulatory RNAs
• Regulatory networks, metabolic networks, proteomic networks
• Cellular signatures of biological responses and disease states
• Phosphorylation, metabolic fluxes, systematic phenotyping
• Mathematical modeling and simulation of biological systems
• Methods for systematic validation of high-throughput biological predictions
• Approaches for aggregation of results arising from different methodologies

We will also be opening conference registration and a call for abstracts very soon.

We hope that you will consider submitting a paper, and look forward to an exciting meeting in November.

Best regards,

Andrea Califano, Manolis Kellis, Sylvia Plevritis, and Gustavo Stolovitzky

Conference Chairs