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Upcoming Conferences

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    The ISCB Affiliates program is designed to forge links between ISCB and regional non-profit membership groups, centers, institutes and networks that involve researchers from various institutions and/or organizations within a defined geographic region involved in the advancement of bioinformatics. Such groups have regular meetings either in person or online, and an organizing body in the form of a board of directors or steering committee. If you are interested in affiliating your regional membership group, center, institute or network with ISCB, please review these guidelines (.pdf) and submit your application using the online ISCB Affiliated Group Application form. Your exploratory questions to ISCB about the appropriateness of a potential future affiliation are also welcome by Diane E. Kovats, ISCB Executive Director (This email address is being protected from spambots. You need JavaScript enabled to view it.).

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Professional Development, Training and Education

ISCBintel and Achievements

Award Winners

Awards and acknowledgments video of Closing Ceremonies

 

ISCB Senior Scientist Accomplishment Award
Michael Ashburner, University of Cambridge, United Kingdom
From sequences to ontologies - adventures in informatics


ISCB Overton Prize Lecture
Olga Troyanskaya
Princeton University , New Jersey, United States
Integrating computation and experiments for a molecular-level understanding of human disease


Ian Lawson Van Toch Memorial Award – Outstanding Student Paper
Sara Berthoumieux
INRIA, France
Identification of metaboloic network models from incomplete high-throughput datasets


JBI Award for the Best Paper in Translational Bioinformatics
Ankur Parikh, Carnegie Mellon University, United States,
Wei Wu, University of Pittsburgh Medical Center, United States
Both authors contributed equally to this paper
TREEGL: Reverse Engineering Tree-evolving Gene Networks Underlying Developing Biological Lineages


Outstanding Poster
Adam Sardar, University of Bristol, United Kingdom
The Darwinian Tree of Life in Light of Horizontal Gene Transfer (Is Still Sound)


RCSB PDB Poster Award
Tammy Cheng, Cancer Research UK
Structural Biology Meets Systems Biology: A Structural Systems Biology Approach for Gauging the Systemic Effect of Single Nucleotide Polymorphisms


Killer App Winner
Syed Asad Rahman, EMBL-European Bioinformatics Institute
ECBlast: a novel tool for searching similar enzymes based on chemical knowledge


Art and Science Award
Anna Dehof, Saarland University, Germany
Reflections on Protein Structures

Honorable Mention:
MajaKlevanski, University of Heidelberg, Germany
Protein Art


Orienteering Winners
Winning Team: Wang, Stelman, Murray &Meintjes
Runner Up: Khan, Seemann, Warsow, Barber

Birds of a Feather (BoF) Schedule

Topic: Computational Biology in Wikipedia

Leader: Alex Bateman
Email:  This email address is being protected from spambots. You need JavaScript enabled to view it.
Affiliation: Wellcome Trust Sanger Institute

Time: Sunday, July 16, 5:30 - 6:30
Room: Hall F1

Description:
Wikipedia is a a widely used resource to learn about Computational Biology. However, the content is of variable quality.  This session aims to develop a task force to improve Wikipedia content in Computational Biology.


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PLoS Conference Postcards
The presenters listed here  have agreed to their work being discussed in Conference Postcards.
If you are attending ISMB 2011 PLoS Computational Biology invites you to send them a postcard! Conference Postcards represent a novel way to report important innovations and current research efforts presented at a scientific conference as told by upcoming members of the scientific community. Your “postcard” will focus on one of the conference presentations - a keynote, paper, poster, technology track demonstration, or tutorial.

Sample articles can be found in the PLoS Computational Biology Conference Postcards collection.
 
All Conference Postcards will be considered by the Editors and those selected will be published in PLoS Computational Biology as part of an article summarizing the conference.
 
If you would like to submit a Conference Postcard, here is what you need to know:
 
  • Any postdoctoral fellow or graduate student is eligible to be an author. Authors may submit more than one report for consideration, but each report may only have one author.
  • Your Conference Postcard should be between 800-1000 words and should not include images or figures.
  • You should include:
    • A synopsis of what was presented.
    • Reasons why you think your chosen presentation is outstanding.
    • How it related to the theme of the meeting.
    • The impact it had on attendees.
    • Additional references considered useful.
  • Any presentation at the conference deemed to be of exceptional significance to the broader community by the author is eligible to be reported. No permission from speakers is required beyond those obtained by ISMB, however, we strongly encourage you to talk with the speaker and check that they have agreed for their presentation to be reported on.
  • Please do not submit reports on presentations given by a close colleague.
  • Preference will be given to reports that demonstrate evidence of additional research into the topic to support or counter the work presented, e.g., views of the work by other attendees gathered through personal interactions or blogs or information based on further discussions with the presenters.
  • Reports accepted by the Editors for publication will be presented as a single article with author ordering determined by the PLoS Editors. PLoS Editors may request that the reporters make (generally minor) changes to the selected reports.
  • As with all PLoS content, the Conference Postcards will be published under the Creative Commons Attribution License Agreement; made freely and fully available immediately upon publication; and deposited in PubMed Central and indexed in PubMed.
  • Please register your interest at contribute[at]plos.org to let us know which session you intend to write about by July 22nd 2011. Submissions or first drafts will be posted on the PLoS Blog upon receipt.
  • Your submission should be sent via email to contribute[at]plos.org with the report in the body of the email or attached as a Word document. Please use “ISMB 2011 Postcards” as the subject of your email. Please include your name, institution, and the title of the session being reported on within both the submitted report and the message text of your email.
  • The closing date for submissions is: August 2nd 2011.

Keynote Presentations


Bonnie Bergeralt
Massachusetts Institute of Technology
Cambridge, United States

Presentation Title: Computational biology in the 21st century: making sense out of massive data

Sunday, July 17 – 9:00 a.m. – 10:00 a.m.

 

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ISCB Overton Prize Lecture

Due to a last minute inability to travel, this talk will be a presented as a pre-recorded video followed by an interactive live feed to Dr. Troyanskaya for Q&A after the presentation.


Olga Troyanskaya alt
Princeton University
New Jersey, United States

Presentation Title: Integrating computation and experiments for a molecular-level understanding of human disease

Sunday, July 17 – 4:30 p.m. – 5:30 p.m.

 

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ECCB 10th Anniversary Keynote

Janet Thornton Janet Thornton
European Bioinformatics Institute
Cambridge, United Kingdom

Presentation Title: The Evolution of Enzyme Mechanisms and Functional Diversity

Monday, July 18 – 9:00 a.m. – 10:00 a.m.

 

 

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ISCB Fellow Keynote

Alfonso Valencia
Alfonso Valencia
Spanish National Cancer Research Centre (CNIO)
Madrid, Spain

Presentation Title: Challenges for Bioinformatics in Personalized Cancer Medicine

Monday, July 18 – 4:30 p.m. – 5:30 p.m.

 

 

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Sponsored by the University of Vienna

Luis Serrano Luis Serrano
Centre for Genomic Regulation
Barcelona, Spain

Presentation Title: M pneumoniae
(Towards a full quantitive understanding of a free-living system)

Tuesday, July 19 – 9:00 a.m. – 10:00 a.m.

 

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ISCB Senior Scientist Accomplishment Award

Michael Ashburner alt
University of Cambridge
United Kingdom

Presentation Title: From sequences to ontologies - adventures in informatics

Tuesday, July 19 – 4:30 p.m. – 5:30 p.m.

 

 

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Workshops

 

Workshop 1: Bioinformatics Core Facilities
Workshop 2: Navigating the Granting Jungle
Workshop 3: Data Visualization and User Interfaces
Workshop 4: Unifying Bio-Resources Descriptors
Workshop 5: Workshop on Education in Bioinformatics (WEB 2011)
Workshop 6: Genomics for Non-Model Organisms

 

Workshop 1: Bioinformatics Core Facilities
 
Organizer(s):
Simon Andrews, Babraham Institute, United Kingdom
Fran Lewitter, Whitehead Institute, United States
Brent Richter, Partners Healthcare, United States
David Sexton, Vanderbilt University, United States

Date: Sunday, July 17
Time: 10:45 a.m. – 12:40 p.m.
Room: Hall N/O

 
 
Workshop Overview
 
This workshop is organized by an international organisation (http://www.bioinfo-core.org) that brings together computational biologists working in and running bioinformatics core facilities. The group was formed in 2002 and draws its membership from over 200 facilities in 23 countries.
 
Bioinformatics core facilities undertake work encompassing the full breadth of modern computational biology. Exposure to varied datasets from many different sources allows us to critically evaluate software and methods from a viewpoint not normally available to research groups.
 
Part A: Analysis Pipelines for high throughput sequencing – what can we learn, and what do we miss?  (25 minutes of talks, 25 minutes of open discussion moderated by Brent Richter, Partners Healthcare)
 
A major goal of the bioinformatics core facility is to deliver high-quality data and tools to the researcher. Standardised pipelines coming either from instrument manufacturers or dedicated bioinformatics groups can provide a simple way to provide analysed data to researchers. However the unsupervised nature of pipelines leads to the possibility that useful and relevant information may be missed. We will explore the potential benefits of automated analysis, but will also investigate what insights might be missed by relying only on standard pipelines. We will address questions such as:
·         Under what circumstances can delivering only the results of a standard pipeline be misleading?
 
·         What is the potential value of the intermediate data calculated in larger pipelines?
 
·         How can we best balance the value of in-depth investigation with the value derived from this extra effort?
 
·         Can pipelines be given to non-bioinformaticians to use in their own data analysis without instruction on the caveats of their use?
 
·         Can pipelines be shared within the community without the need to adapt them to each individual environment?
 
Speakers
Simon Andrews (Head of Bioinformatics, Babraham Institute) will present a series of case studies derived from two tools developed in his group; FastQC – a tool which analyses raw high throughput sequence data to identify trends and biases which might not appear in later analysis of mapped data, and a repeat mapping pipeline which provides a mechanism by which aggregate data on multiply mapping reads to be collected and analysed.
 
Jim Cavalcoli (Bioinformatics Core Director, University of Michigan) will present the results of two RNA-Seq studies, where data that were originally rejected as unmappable was reanalysed to reveal insights about transposable elements and non-standard splicing mechanisms.
 
 
Part B: Practical aspects of running a bioinformatics core facility (25 minutes of talks, 25 minutes of open discussion moderated by Fran Lewitter, Whitehead Institute)
 
We will explore the practicalities of providing a bioinformatics service to a large group of researchers. It will look at how such groups are structured, funded, staffed and monitored. The aim of the session is to share best practices and to stimulate discussions on how these facilities can achieve the best scientific results in the most efficient way.

Speakers
 
Matthew Eldridge (Head, Bioinformatics Core, Cancer Research UK, Cambridge Research Institute). The CRI Bioinformatics Core provides computational and statistical support to 21 research groups, with approximately 270 scientists, whose interests’ range from pure basic research questions to clinical applications with practical benefits for cancer patients.
 
Simon Lin (Bioinformatics Consulting Core Director, Northwestern University) The Northwestern Bioinformatics Core Facility provides analysis, support and design for next generation sequencing, microarrays, proteomics, clinical trial informatics as well as custom web-based database development for basic science and clinical projects. The goal is to provide researchers with in-house expertise of bioinformatics in order to produce studies that ultimately result in publications and grants.
 
 
 
Workshop 2: Navigating the Granting Jungle

 

Organizer(s):
Yana Bromberg, Rutgers University, United States
Magali Michaut, University of Toronto, Canada
Venkata P. Satagopam, EMBL, Germany
Andrea Schafferhans, TU Münich, Germany

Date: Sunday, July 17
Time: 2:30 p.m. – 4:25 p.m.
Room: Hall N/O

 
Workshop Overview
 
Many different agencies provide funding for research activities. These exist on national levels, but also fund bi-national or international co-operation. This workshop will help current and future principle investigators from the field of bioinformatics and computational biology to get an overview of funding options and information resources available to find such funding sources. In addition, the workshop will help select those funding schemes that are promising as fitted to the individual situation (career stage, collaborators, etc).
 
The proposed workshop in Grant writing is meant to complement the Tutorial on Grant writing to be given on July 15th, 2011. While the tutorial focuses on how to write a grant application, the primary aim of the workshop will be to point researchers to the available funding options. The workshop will consist of a panel discussion and 6 invited presentations (12 min each with time for questions) on the following topics:
A)     Overview of funding options (individual grants, group funding, integrated projects, etc.)
B)      Experiences and recommendations from the reviewers’ point of view
C)      How to find applicable grants and how to choose which ones to apply for
 
 
Speakers
  • Gary Bader is an Assistant Professor at the University of Toronto
  • Phil Irving is the Head of Grants Services, European Molecular Biology Laboratory (EMBL)
  • Andrew L. Hufton works at EMBO as an Editor for Molecular Systems Biology Journal
  • Lawrence Hunter is the Director of the Centre for Computational Pharmacology & Computational Bioscience Program
  • Michal Linial is the Director of the Sudarsky Center for Computational Biology,  the Hebrew University of Jerusalem, Israel
  • Alfonso Valencia is the Director of the Spanish National Bioinformatics Institute (INB)
Programme Time Table
 
Time
Topic
Referent
2:30 p.m. - 2:55 p.m.
Funding availability
Andrew L. Hufton, Phil Irving
5 min break
3:00 p.m. - 3:25 p.m.
Reviewer’s recommendations
Michal Linial, Alfonso Valencia
5 min break
3:30 p.m. - 3:55 p.m.
Speaking from experience
Lawrence Hunter, Gary Bader
5 min break
4:00 p.m. - 4:25 p.m.
Finding/selecting funding schemes
Panel discussion with the previous speakers
 
Qualification of the submitter(s) to organize the workshop
 
Yana Bromberg is an assistant professor at Rutgers University, School of Environmental and Biological Sciences. She is the chair of the ISMB poster session, co-organizer of the SNP-SIG, and an active participant on a number of scientific conference and journal review boards. In her 10 years in the field, Yana had been funded through traditional (T15 and R01 mechanisms of the NIH/NLM) and through more exotic sources (SBIR R43, Private funding). In her new position she is looking forward to learning more about the available resources that will support her ongoing research.
 
Magali Michaut is a postdoctoral researcher at the University of Toronto. She has been highly involved with the ISCB Student Council for 4 years, in particular in the organization of the Student Council Symposium (reviewing committee 2008, speaker chair 2009, symposium co-chair 2010, ESCS1 chair 2010). She was one of the elected members (secretary) of the Student Council in 2009, initiated the RSG Europe (secretary) and created and chaired the RSG France.

Venkata P. Satagopam is a Senior Bioinformatics Scientist at EMBL. He is involved with ISCB student council since formed in 2004, particularly in the organization of several student council symposiums, initiated internships for students from developing nations etc. He is also involved in the organization of the Bioinformatics workshops at EMBL and organizing committee member of the ‘Bioinformatics to Systems Biology 2010 conference’.
 
Andrea Schafferhans is a postdoctoral researcher at the TU Munich. In her academic and industrial research positions, she has been involved in applications for national and European funding. As a researcher in the transition to independence she is gathering experience in navigating the funding agency jungle – with a special focus on non-standard careers including industry and family phases.

 
 
Workshop 3: Data Visualization and User Interfaces

 

Organizer(s):
Nils Gehlenborg, Harvard Medical School, United States
Lawrence Hunter, University of Colorado, United Kingdom
Seán O'Donoghue, European Molecular Biology Laboratory, Germany
James Procter, University of Dundee, United Kingdom

Date: Monday, July 18
Time:
10:45 a.m. – 12:40 p.m.
Room:
Hall N/O

 
Workshop Overview
 

This workshop is aimed at ISMB attendees who develop interactive tools or methods to help biologists gain insight from data. Three expert speakers will cover principles, illustrative examples, and resources that can help to improve the effectiveness of data visualization, to improve the usability of user interfaces, and finally to help ensure that users find your tool truly helpful in their research. As biology is becoming increasingly data-driven, and as data volume and complexity increase, the above topics are becoming more relevant and urgent for bioinformatics tool developers. The workshop will consist of three 30 minute talks followed by a 30 minute discussion session, as outlined below.

Part A: 10:45 - 11:10    User Interface Design (Speaker: Scooter Morris). For many computational systems, including bioinformatics tools, ease-of-use can greatly influence the extent to which the end-user community either adopts the tool, or ignores it. This talk will outline key principles that can improve user interfaces, and present several case studies highlighting these principles.

Part B: 11:15 - 11:40    Data Visualization (Speaker: Nils Gehlenborg). Data visualization can be a powerful tool to explore large and complex data sets for hypothesis generation. This talk will outline strategies for the design and implementation of interactive visualizations and highlight successful applications of visualization in bioinformatics. The talk will also address the basic principles of data visualization and discuss some of the challenges that developers face in practice.

Part C: 11:45 - 12:10    Visual Analytics (Speaker: Carsten Görg). The interpretation of biological data is a complex process, involving many different data analysis techniques, often applied in multiple different combinations. Visual analytics tools combine the process of analysis and visualization, and this talk will highlight key tools that enable the researcher to visually analyse and identify significant aspects of their results.

Part D: 12:15 - 12:40    Discussion Session (Moderator: Seán O’Donoghue). Workshop participants will have the opportunity to discuss practical aspects of data visualization, interface design and visual analytics tools with the speakers. In addition to the above speakers, several developers of widely-used software tools have been invited to be part of this session to answer questions from the audience and to share their insights.

 
 
 Workshop 4: Unifying Bio-Resources Descriptors


Organizer(s):
Dawn Field, NERC, NEBC, United Kingdom
Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland
Susanna-Assunta Sansone, University of Oxford, United Kingdom

Date:  Monday, July 18
Time: 2:30 p.m. – 4:25 p.m.
Room: Hall N/O
 

Workshop Overview:

This workshop will bring together developers, curators, journal editors and researchers to discuss on the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications. The focus on the workshop is a strawman uniform system for describing these bio-resources, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement.
Such uniform system will i) assist the research and bioinformatics communities to locate and access the information distributed in these bio-resources and ii) inform journal editors and funders, implementing data preservation, management and sharing policies, when recommending or requiring that certain standards are met and that data is deposited to a public database.
 
Background
High-throughput approaches in genomics and functional genomics bioscience domain have become ubiquitous in the past decade. Several policies have emerged in response to the increased quantity of data available and the correspondingly large variability in their storage and analysis1. The need to store and share this data helps explaining the explosion in the number and variety of tools and databases that cater to the needs of biological research. Many of those resources have contributed to the development of community-level standards that support the harmonization of the annotation and storing process, so that different data can be comprehensible (in principle), reproducible, but also easily shared, analyzed, compared and integrated. The next challenge is to better integrate those policies and standards and link them to the relevant tools and databases implementing them. The goal is to present researchers with a portfolio of standards and resources to enable use and promote adoption. The grand vision is to ease data management and enable data exchange, shielding researchers from unnecessary complexity, and ultimately facilitate data analysis.
The International Society for Biocuration (ISB) and the BioSharing initiative have already taken steps in this direction by i) producing BioDBcore, a community-defined, uniform, generic description of the core attributes of biological databases and ii) releasing a first prototype of “one-stop shop” BioSharing catalogue for those seeking data sharing policy documents and information about the standards. BioDBcore has been developed and published with a wider list of contributors, including NAR and DATABASE editors and published in both journals2 (Gaudet et al. 2011). The catalogue of policies and standards, an outcome of a Special Interest Group (SIG)3 at ISMB 2010, works to link to exiting complementary portals, such as MIBBI4, but also open access resources, such as BMC Research Notes and Nature Precedings, with documents or publications on standards, but also standards-compliant systems and research data.
Combined, BioDBcore and BioSharing efforts will enable existing and emerging resources - cataloguing tools and database - to have a uniform system for describing the biological databases and indicating what standards they implement.
 
Workshop Objectives
At the workshop we will provide updates as to the status of the progresses of how BioDBcore core attributes and the BioSharing catalogues can be used in combination, to unify the description of bio-resources and seek input as to the future of these resources. In addition, the mechanism to exchange the descriptors will be discussed, providing an opportunity for the many interested participants to engage in community assessment and planning for these new efforts. To engage key stakeholders, we will open discussion to emerging efforts working to incorporate BioDBcore descriptors and link to relevant standards catalogued by BioSharing.
 
References
1. Field, Sansone et al. ‘Omics Data Sharing, Science 9, 234 (2009).
2. Gaudet, Bairoch, Field, Sansone et al. Towards BioDBcore: a community-defined information specification for biological databases. Database 4 2011:baq027; and Nucleic Acids Res, 39(Database issue):D7-10 (2011).
3. Field, Sansone et al. Meeting Report: BioSharing at ISMB 2010,Standards in Genomic Sciences, 3 (2010).
4. Taylor, Field, Sansone et al. MIBBI: A Minimum Information Checklist Resource, Nat. Biotechnol. 26, 889 (2008).
 
Agenda
Time Presentation Title
Presenting Author
2:30 p.m. - 3:00 p.m. Unifying Bio-Resources Descriptors - Introduction & BioSharing [abstract]

Susanna-Assunta Sansone, Sansone, University of Oxford

Dawn Field, UK NERC Bioinformatics Data Center

3:00 p.m. - 3:15 p.m. BioDBcore: a community-defined information specification for biological databases Pascale Gaudet, Swiss Institute of Bioinformatics
3:15 p.m. - 3:30 p.m. BioDBcore: moving toward implementation Philippe Rocca-Serra, University of Oxford
3:30 p.m. - 4:25 p.m. Unifying Bio-Resources Descriptors - Panel Discussion - Nicolas Le Novère, MIRIAM resource
- Naomi Attar, BioMedCentral
- Myles Axton, Nature Publishing Group
-
Adriaan Klinkenberg, Elsevier
- Rebecca Lawrence, F1000
- Francis Ouellette, DATABASE and Bioinformatics Link Directory
- Jeffrey Grethe, Neuroscience Information Network 
 
Unifying Bio-Resources Descriptors
This workshop will bring together developers, curators, journal editors and researchers to discuss on the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications. The focus on the workshop is a strawman uniform system for describing these bio-resources, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement.

Such uniform system will i) assist the research and bioinformatics communities to locate and access the information distributed in these bio-resources and ii) inform journal editors and funders, implementing data preservation, management and sharing policies, when recommending or requiring that certain standards are met and that data is deposited to a public database.

BioSharing: http://biosharing.org
bioDBcore: http://biocurator.org/biodbcore.shtml
 

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 Workshop 5: Workshop on Education in Bioinformatics (WEB 2011)

 

Organizer(s):
Michelle Brazas, Ontario Institute for Cancer Research, Canada
Fran Lewitter, Whitehead Institute for Biomedical Research, United States
Andrea Schafferhans, TU München, Germany
Vicky Schneider, EMBL-EBI, United Kingdom
 
Date:  Tuesday, July 19
Time: 10:45 a.m. – 12:40 p.m.
Room:  Hall N/O
 
Workshop Overview:
 
The Workshop on Education in Bioinformatics (WEB 2011) is for ISMB attendees who are involved in training, education and teaching. The workshop will provide a platform to listen from experienced experts and discuss the following topics relevant to the continued advancement of this field:
1)         The key elements required of a good bioinformatics tutorial;
2)         How bioinformatics tutorials and training materials can be used in remote training;
3)         Sharing of training related materials.
 
 
Time Table
Time
Speakers/Panellists
Part A:
10:45 a.m. - 11:10 a.m.
Dr. Anna Tramontano
Dr. Gary Bader
Part B:
11:15 a.m. - 11:40 a.m.
 
Panel discussion lead by Dr. Fran Lewitter
Part C:
11:45 a.m. - 12:10 p.m.
Dr. Aidan Budd
Dr. Alex Bateman
Dr. Vicky Schneider
Part D:
12:15 p.m. - 12:40 p.m.
Panel discussion lead by Dr. Michelle Brazas (Panel composed of all WEB11 contributing speakers)
 
 
Part A: Effective Bioinformatics Training: what makes a good tutorial
Bioinformatics Training is challenging not only because of the interdisciplinary nature of the field and audience, but also because the current rapid technological advances demand new and increasingly complex bioinformatics tools. Educational materials must be constantly updated and produced to meet training needs. Solutions that increase development and dissemination of useful and effective learning tools, and increase access and uptake of bioinformatics training would benefit the bioinformatics community as a whole.
 
Increased exposure of bioinformatics training content in peer-reviewed journals would benefit bioinformatics training efforts as well as the scientific community at large. Experts in Bioinformatics training will present their views. This will be followed by a discussion of what constitutes a ‘good tutorial’ which would help define the landscape for the development and dissemination of effective bioinformatics training material in the future.
 
Part B: Panel Discussion, Gary Bader, Anna Tramontano, Andrea Schafferhans, Moderator: Fran Lewitter
 
Part C: Effective sharing of training efforts: from the materials to the live session
As effective training materials are developed and disseminated, such materials may be used to expand bioinformatics training to researchers in more remote locations where face-to-face training is costly and prohibitive. Speakers will discuss their own experiences with remote training, as well as using Wikipedia and other databases to share training materials. A discussion of how technology enables such training would follow. The aim will be to define the landscape for expanding bioinformatics education and awareness to the wider scientific community.
 
Part D: Panel Discussion, Gary Bader, Alex Bateman, Aidan Budd, Vicky Schneider, Anna Tramontano, Moderator: Michelle Brazas
 

Panellist Chairs:
Dr. Fran Lewitter
Dr. Michelle Brazas
 
Confirmed speakers include:
Dr. Gary Bader (University of Toronto)
Dr. Alex Bateman (Wellcome Trust Sanger Institute)
Dr. Aidan Budd (EMBL-Heidelberg)
Dr. Anna Tramontano (Universita La Sapienza)
Dr. Vicky Schneider (EMBL-EBI)

 
Workshop 6: Genomics for Non-Model Organisms

Organizer(s):
Dave Clements, Emory University, United States
 
Date:  Tuesday, July 19
Time: 2:30 p.m. – 4:25 p.m.
Room:  Hall N/O

Workshop Overview:
 

This workshop will demonstrate implemented, successful approaches to several common challenges when working with genomic data from non-model organisms. Early genomics work focused on well established model organisms and built on the availability of robust resources such as high-quality annotated reference genomes and manually curated online model organism databases.  This workshop will highlight recent advances in working with genomic data when you don't have access to the rich resources that come with well-established model organisms.

2:30 p.m. - 2:55 p.m.  Using RAD-seq for genomic and transcriptomic studies of non-model organisms, Julian Catchen
3:00 p.m. - 3:25 p.m. Using RNA-seq for gene annotation, quantitation, and function in non-model organisms, Jeremy Goecks
3:30 p.m. - 3:55 p.m.  Development of a workflow for SNP detection in grapevine species: MAPHiTS, Marc Bras
4:00  p.m. - 4:25 p.m.  Repeatable plant pathology bioinformatic analysis: not everything is NGS data, Peter Cock


Part A: Using RAD-seq for genomic and transcriptomic studies of non-model organisms
Julian Catchen (presenting) and William Cresko, University of Oregon, United States

We have developed novel next generation sequencing protocols for high-throughput genotyping and allele-specific profiling in organisms with or without prior genomic resources. Our technique, Restriction-site Associated DNA sequencing (RAD-seq), focuses high-throughput sequencing effort on regions of the genome adjacent to restriction enzyme recognition sites. RAD-seq enables the construction of genetic maps, genome contig tiling, QTL and association mapping, and studies of evolutionary processes in natural populations. We will discuss 1) the suite of RAD molecular biology techniques with examples from non-model organisms; 2) analytical and computational tools that we have developed, encapsulated in the software package Stacks, for the analysis of RAD-seq; and 3) the major remaining challenges for applying techniques like RAD to studies in non-model organisms.

Part B: Using RNA-seq for gene annotation, quantitation, and Function in non-model organisms
Jeremy Goecks, Emory University, United States

A primary use of RNA-seq data from a non-model organism is to gain insight into the organism's genes.  Specifically, it is often useful to annotate a genome assembly with gene locations; also, regardless of whether a genome assembly is available, it is useful to quantitate the expression of genes and predict their likely function. Using multiple tools, including Cufflinks, Trans-ABySS, and Galaxy, we have developed methods and pipelines for performing gene annotation, quantitation, and predicting function. We will discuss a case study where we have analyzed RNA-seq data from four related organisms to characterize the similarities and differences in gene expression amongst the organisms.


Part C: Development of a workflow for SNP detection in grapevine species: MAPHiTS
Marc Bras, INRA-URGI, Centre de Recherche de Versailles-Grignon, France

A Single-Nucleotide Polymorphism (SNP) is a DNA sequence variation. It can be used as a marker to characterize genetic variations. They can be used to detect complex traits such as those involved in diseases resistance or agronomical performance. The URGI platform developed a workflow for SNPs detection from short reads (MAPHiTS: Mapping Analysis Pipeline for High-Throughput Sequences), integrated in the Galaxy workflow manager. Galaxy allows, through a web page, to chain different tools graphically. In addition, a large number of workflows can be built and shared. MAPHiTS workflow is able to deliver all SNPs and small indels found in the data set and to filter them according to various parameters such as the genome coverage, the allele frequency and pValue.


Part D: Repeatable plant pathology bioinformatic analysis: not everything is NGS data.
Peter Cock (presenting), Leighton Pritchard, James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), United Kingdom

The James Hutton Institute's Plant Pathology programme studies a wide range of biological kingdoms and diverse pathogens of great social impact.  We are interested in high throughput sequencing data, but our principal use for Galaxy is to provide a framework to deliver standardised, reusable components for repeatable bioinformatic analyses of assembled sequences and gene sets. We aim to empower bench scientists to carry out their own complex bioinformatic analyses and construct workflows.  We present examples of the  integration of bioinformatic tools using the Galaxy framework, and common workflows for plant pathology, such as identifying candidate proteins that are delivered by pathogens into their hosts - an important mechanism for pathogens and parasites.

 

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Special Session Details

ISMBECCB 2011 features Special Session presentations throughout the conference July 17 - July 19. Special Sessions have the purpose of introducing the scientific community to relevant scientific issues and topics that are typically not within the focus of the conference. Preliminary program information on Special Sessions is noted below. (Schedule subject to change)

Special Session 1: BioLINK: Integration across Genomics and Medicine

Organizer(s):
Christian Blaschke, Bioalma, Madrid, Spain
Lynette Hirschman, Mitre, Bedford, United States
Hagit Shatkay, University of Delaware, United States
Alfonso Valencia, Spanish National Cancer Research Centre, Madrid, Spain

Date:  Sunday, July 17
Start Time:  10:45 a.m. - 12:40 p.m.
Room: Hall F2
 
Description:

This year, the BioLINK meeting reaches out to the diverse ISMB community with a highly relevant interdisciplinary topic: data integration and interoperability across the computational, biological and medical fields. Instead of the traditional one-day SIG before ISMB, which typically focused on various aspects of text mining, this year we take a broad focus at the interface of bioinformatics and medicine, and we are holding the meeting as a special session within the conference.

Much information in both biology and medicine exists in the form of text, including reports, published literature, database entries and medical patient records. Hence, text mining methods (which have traditionally been the focus of BioLINK) remain relevant to both the biological and the medical communities, and to the interdisciplinary research between the two.
However, many other types of relevant data, ranging from genomic mutations to chemical reactions and vital signs in patients are not textual. They come in the form of time series, images, genomic and proteomic sequences, among others.

Translating biological advances into practical medical solutions is the focus of much current research in several communities, and discussions of the needs and the challenges have recently been taking place at AMIA, particularly at the Summit on Translational Bioinformatics, as well as in the EU, at the workshop on Bridging the Gap in Biomedical Genetics (October, 2010, Cambridge, UK). This special session is specifically centered on the role and challenges of multiple types of data and models, and the way such diverse sources of information can be integrated and used effectively.

Talks and Speakers:

10:45-10:50

 Session Introduction

10:50-11:10

Speaker: Soren Brunak, PhD.
                   Technical University of Denmark &
                    University of Copenhagen

Title:
Integrating phenotypic data from electronic patient records with molecular level systems biology

11:10-11:15

Transition to parallel tracks

11:15-11:40

Speaker: Russ Altman, MD, PhD.
                        Stanford University

Title:
Issues in annotating whole-genome data with clinically relevant pharmacogenomics knowledge

 11:40-11:45

Transition to parallel tracks

11:45-12:10

Speaker: Yves Moreau, PhD.

                   Katholieke Universiteit Leuven                         

Title: 
Instrumenting the Healthcare System to Define the True Names of Disease

 12:10-12:15

Transition to parallel tracks

12:15-12:40

Panel Discussion (Drs. Altman, Brunak and Moreau)
Interoperability across Information Extraction and Computational Bio-medicine Platforms

Led by Florian Leitner, CNIO, Spain,
and Karin Verspoor, PhD, University of Colorado, Denver

 

Talk Abstracts and Speakers Bios:

Integrating Phenotypic Data from Electronic Patient Records with Molecular Level Systems Biology
Speaker:Søren Brunak, Technical University of Denmark & University of Copenhagen
 
 
Abstract: Electronic patient records remain a rather unexplored, but potentially rich data source for discovering correlations between diseases. We describe a general approach for gathering phenotypic descriptions of patients from medical records in a systematic and non-cohort dependent manner. By extracting phenotype information from the free-text in such records we demonstrate that we can extend the information contained in the structured record data, and use it for producing fine-grained patient stratification and disease co-occurrence statistics. The approach uses a dictionary based on the International Classification of Disease ontology and is therefore in principle language independent. As a use case we show how records from a Danish psychiatric hospital lead to the identification of disease correlations, which subsequently are mapped to systems biology frameworks.
 
BIO:
Søren Brunak, Ph.D., is professor of Bioinformatics at the Technical University of Denmark and professor of Disease Systems Biology at the University of Copenhagen. Prof. Brunak is the founding Director of the Center for Biological Sequence Analysis, which was formed in 1993 as a multi-disciplinary research group of molecular biologists, biochemists, medical doctors, physicists, and computer scientists. Søren Brunak has been highly active within data integration, where machine learning techniques often have been used to integrate predicted or experimentally established functional genome and proteome annotation. His current research does combine molecular level systems biology and healthcare sector data such as electronic patient records and biobank questionnaires . The aim is to group and stratify patients not only from their genotype, but also phenotypically based on the clinical descriptions in the medical records.
Prof. Brunak completed his early studies in physics at the Niels Bohr Institute, University of Copenhagen, and his doctoral work in Computational Biology at the Technical University of Denmark. Brunak has published more than 175 papers with peer-review, altogether having more than 18,500 citations. His most cited paper (from 1997) has more than 3,800 citations, h-factor 53. Søren Brunak is member of the Danish Academy for the Natural Sciences (1997), The Danish Academy of Technical Sciences (2002), The Danish Royal Society of Science and Letters (2004) and of EMBO since 2009. More about his research group can be found at www.cbs.dtu.dk.
 
 
Issues in Annotating Whole-Genome Data with Clinically Relevant Pharmacogenomics Knowledge
Speaker: Russ Biagio Altman. Professor of Bioengineering, Genetics, & Medicine; Chairman of the Bioengineering Department. Stanford University.
 
 
Abstract:  The mission of the Pharmacogenomics Knowledgebase (PharmGKB, http://www.pharmgkb.org/) is to collect and encode all available information about how human genetic variation impacts drug response.  We have recently reported using the PharmGKB to annotate the whole genome of an individual.  This initial annotation was done manually and taught us what would be required for routine markup of genomes in a relatively high-throughput fashion.   We have therefore revisited much of the PharmGKB contents and re-curated the data in order to make clinical annotation more facile and accurate.   I will discuss the issues associated with annotating whole human genomes, particularly focusing on the challenges of annotating rare or novel mutations that have never been (and may never be) studied, but which look potentially important for the individual whose genome is being annotated. 
 
BIO:
Russ Biagio Altman is professor of bioengineering, genetics, & medicine (and of computer science, by courtesy) and chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing technology to basic molecular biological problems of relevance to medicine. He particularly interested in informatics methods for advancing pharmacogenomics, the study of how human genetic variation impacts drug response (e.g. http://www.pharmgkb.org/). Other work focuses on the analysis of functional sites within macromolecules  and the application of algorithms for determining the structure, dynamics and function of biological macromolecules (http://features.stanford.edu/). Dr. Altman holds an M.D. from Stanford Medical School, a Ph.D. in Medical Information Sciences from Stanford, and an A.B. from Harvard College. He has been the recipient of the U.S. Presidential Early Career Award for Scientists and Engineers and a National Science Foundation CAREER Award. He is a fellow of the American College of Physicians, the American College of Medical Informatics, and the American Institute of Medical and Biological Engineering. He is a past-president and founding board member of the International Society for Computational Biology, and an organizer of the annual Pacific Symposium on Biocomputing. He leads one of seven NIH-supported National Centers for Biomedical Computation, focusing on physics-based simulation of biological structures (http://simbios.stanford.edu/). He won the Stanford Medical School graduate teaching award in 2000. He is a member of the Institute of Medicine of the National Academies
 
 
Instrumenting the Healthcare System to Define the True Names of Disease

Speaker: Yves Moreau, Katholieke Universiteit Leuven                         


Abstract:  Most disciplines of medicine, with the notable exception of infectious disease, continue to classify and treat disease at the phenomenological level. The promise of genomic medicine includes personalizing diagnoses and therapies but also of redefining diseases based on molecular markers to bring us closer to an etiological classification. The availability of commodity-priced genome-scale assays and large public data sets makes the goal of finding these “true names” of diseases now feasible. Several such approaches are described ranking from cancer to autism. Also discussed are several structural impediments achieving this goal including: A) the growth of the Incidentalome, the tsunami of false positives that inevitably result from application of massively parallel tests; B) the lack of systematic interpretations of genomic tests and evaluation of their performance C) the absence of a mechanism to transfer the growing knowledge of genomics to the physician at the point of care. The opportunity in instrumenting the healthcare enterprise for discovery research to overcome these impediments is reviewed.

 
About the Organizers:
 
Christian Blaschke is technical coordinator of the Spanish Institute of Bioinformatics (INB), Madrid, Spain. He obtained his PhD in the Group of Alfonso Valencia and was part of the organization of BioLINK SIG meetings starting in 2002. His academic work has been focused on text mining applied to molecular biology and biomedicine where he contributed in the areas of protein-protein interactions, DNA array analysis and automatic ontology learning. Christian Blaschke was also one of the organizers of the BioCreAtIvE (Critical Assessment of Information Extraction for Biology) challenge carried out in 2004.
 
 
Lynette Hirschman is Director, Biomedical Informatics for the Information Technology Center at the MITRE Corporation in Bedford, MA, USA. She has been an organizer of the BioLINK SIG on Text Mining in Biology for ISMB starting in 2002. and a founder of BioCreAtIvE, (Critical Assessment of Information Extraction for Biology), the first Challenge Evaluation for text mining applied to biological applications. Her research focuses on the application of natural language processing technology to biomedical applications, including removal of personally identifiable information (PII) for protection of privacy, automated fact extraction for medical records and on the coupling of genomic and clinical data to support translational medicine. She is a member of the board of the Genomic Standards Consortium, working on metadata capture for metagenomics and a member of the organizing team for the i2b2 2011 challenge evaluation for information extraction from medical records.
 
Hagit Shatkay is an Associate Professor at the Dept. of Computer and Information Sciences at the University of Delaware, with cross-appointments at the Biomedical Engineering Program, and at the Delaware Biotechnology Institute. Her research is in the area of machine learning as it applies to biomedical data mining. Among her many organizational roles, she has been on the organizing committee of the BioLINK SIG at ISMB since 2005, on the steering committee for TREC Genomics, and multiple times chair of the text mining area at ISMB.
 
She is an active member of the bio-text research community since its early days (1999), where her work focuses primarily on biomedical information retrieval, and more recently on integrating text, image and sequence data within the biological data mining process. Recent major projects in her lab include work on understanding and predicting heart disease using multiple sources of information, document retrieval through image and text data, SherLoc – protein subcellular location prediction by integrating text and sequence data, and F-SNP – a comprehensive system for ranking SNPs by potential deleterious effects.  

 Alfonso Valencia is the director of the Structural and Computational Biology Programme of the Spanish National Cancer Research Centre and Director of the Spanish Bioinformatics Institute. His group works in the development and application of Computational Biology methods for the study of problems related with the evolution of molecular interactions. In the field of text mining his group developed new approaches for the detection of protein function and interactions in biological text and a number of applications combining text mining with other genomic resources.

Dr. Valencia is co-executive editor of the journal "Bioinformatics", member of EMBO, co-organizer of ECCB 05, chair of the text mining/Biological networks areas of ISMB (03-07) and founder, former VP, and member of the board of directors of ISCB. Dr. Valencia has been part of the organization of BioLINK (Text Mining in Biology) since 2001 and co-organizer of the Critical Assessment of Information Extraction for Biology (BioCreAtIvE 2003-4, 2006-07, 2009-2012).

 

 

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Special Session 2: Insights & outlook for individual genome interpretation: lessons from the Critical Assessment of Genome Interpretation
Organizer(s):
John Moult, Baltimore, University of Maryland, United States
Susanna Repo, University of California, Berkeley, United States
Steven E. Brenner, University of California, Berkeley, United States
 
Date:  Sunday, July 17
Start Time: 2:30 p.m. – 4:25 p.m.
Room:  Hall F2

Description:
This session will provide an overview and assessment of the state-of-the art in prediction of phenotype from genotype. The session is motivated by the burgeoning availability of individuals' genomes, and the desire to interpret them for research and clinical applications.

The Critical Assessment of Genome Interpretation (CAGI, \'kā-jē\), is a community experiment to assess the current methods of predicting phenotypic impacts of genomic variation. Based on the same model as CASP (Critical Assessment of Structure Prediction), the experimental goals of CAGI are to evaluate the current methods to make useful predictions of phenotypes from genomics data, to identify bottlenecks in genome interpretation that suggest especially critical areas of future research, and to engage and connect researchers from the diverse disciplines whose expertise is essential to methods for genome interpretation.

The first round of CAGI, which was organized during the latter half of 2010, included predictions of phenotype for two sets of cancer mutations, a set of mutations in a monogenic disease related enzyme, 10 personal genomes, and identification of the molecular mechanisms underlying the results of genome wide association studies. In total, 108 prediction submissions from 17 research groups in 8 different countries were submitted to the first CAGI experiment.

In this session, an overview of the initial CAGI experiment will be presented. We will discuss the broad successes and failures, and describe the prediction challenges of the different datasets of CAGI. Current methods for predicting phenotype from genomic data will be presented and the limitations of these methods discussed. The future directions for CAGI and genome interpretation will also be discussed.
 
 
Finalized Schedule
 
Timeline:
 
2:30PM Introduction to the Critical Assessment of Genome Interpretation (CAGI) experiment
2:50PM Discussion
2:55PM Transition to parallel tracks
3:00PM Results from CAGI 2010: successes and challenges
3:20PM Discussion
3:25PM Transition to parallel tracks
3:30PM Methods to predict individuals’ medical phenotypes from genomic data
3:50PM Discussion
3:55PM Transition to parallel tracks
4:00PM Future directions for CAGI and Genome Interpretation, Panel Discussion
4:20PM Conclusions on panel discussion
4:25PM Transition to parallel tracks
 
 
Session descriptions:
 
Introduction to the Critical Assessment of Genome Interpretation (CAGI)  experiment
 
Speakers:
Steven E. Brenner, University of California Berkeley
Susanna Repo, University of California Berkeley
 
In this session, CAGI organizers will provide an introduction to the experiment and survey the mechanisms by which genetic variation can yield phenotypic impacts and will define the different levels of phenotypes – organismal, cellular and molecular – that are predicted in the CAGI effort. The speakers will discuss variation phenomena, observation methods and resulting data, and exemplary biological phenotypes that result from each. The first CAGI experiment will also be described, with a description of the prediction datasets of that experiment.
 
Results from CAGI 2010: successes and challenges

Speaker: Pauline Ng, Genome Institute of Singapore

Pauline Ng, an assessor for CAGI , will present an overview of results of the initial experiment. She will discuss broad successes and failures, and describe the prediction challenges of the different CAGI datasets, focusing on the single nonsynonymous variations. She will identify bottlenecks of the current methods and datasets and suggest future research directions.
 

Methods to predict individuals’ medical phenotypes from genomic data           

 Speakers:      
Sean Mooney, Buck Institute 
Rachel Karchin, Johns Hopkins University
Hannah Carter, Johns Hopkins University

 

One of the most challenging CAGI datasets involved predicting the phenotypes of individuals from the Personal Genome Project.  These individuals have made many of their genomes and medical characteristics publicly available.  We solicited dozens of additional as-yet unpublished phenotypes from these individuals and presented these to predictors.  The assessor for this dataset, Sean Mooney, will present an overview of the challenge and the nature of the results.  Hannah Cater and Rachel Karchin will be shown in a video explaining their approach to making predictions for this dataset. 

 
Future directions for CAGI and Genome Interpretation, Panel Discussion
 
Panel members:
Russ Altman, Stanford University
Rita Casadio, University of Bologna
Iddo Friedberg, Miami University
Mauno Vihinen, University of Tampere
John Moult, University of Maryland (Discussion moderator)
 
In this last session, panelists will discuss the future directions for CAGI and genome interpretation. In order to facilitate the participation of the ISMB community in the discussion, we will collect questions, comments, and suggestions from the audience throughout the special session using electronic communications.
 
 
 

 
Special Session 3: RNA structure: from genomes to nanotechnology
Organizer(s):
Peter Clote, Boston College, United States
Ivo L. Hofacker, University of Vienna, Austria
David Mathews, Rochester Medical Center, New York, United States
Peter Schuster, Professor emeritus, University of Vienna, Austria

Date:  Monday, July 18
Start Time:  10:45 a.m. – 12:40 p.m.
Room:  Hall F2

Description:
This Special Session includes both computational and experimental methods at the cutting edge of RNA research. The interdisciplinary aspects are focusing on theory and practice to engineer and control RNA molecules for performing computations, for controlling genes, for self-assembly, for binding as aptamers to specific targets, and ultimately for serving as pharmaceuticals.
 
Speakers:
  • Niles Pierce, Caltech
  • Rhiju Das, Stanford
  • Susan Gottesman, NIH
  • Peter Stadler, Leipzig

Title:

Engineering Nucleic Acid Devices

Speaker:

Niles Pierce, Caltech

Abstract:

The programmable chemistry of nucleic acid base-pairing provides a versatile framework for engineering molecular devices and systems. This talk will describe efficient algorithms for nucleic acid sequence design and illustrate their use in engineering programmable molecular amplifiers for multiplexed imaging of mRNA expression within intact vertebrate embryos.


Title:
Atomic accuracy and blind predictions through enumerative 3D RNA modeling

Speaker:
Prof Rhiju Das, Stanford

Abstract:
High-resolution 3D structure modeling of RNAs and other macromolecular systems is a long sought but still unachieved goal of computational biology. Inspired by successful protein modeling approaches, we recently showed that the Rosetta framework permits modeling and design of small non-canonical RNA motifs at near-atomic accuracy. Nevertheless, a major bottleneck remains: the difficulty of comprehensively sampling these molecules’ many degrees of freedom. Towards eliminating fundamental issues in this sampling bottleneck, we have postulated a ‘StepWise Ansatz’ (SWA) for constructing well-packed models in small steps, enumerating several million conformations for each nucleotide and covering all possible build-up paths. We present results on non-canonical RNA motifs as well as highly irregular protein loops that have been intractable for prior fragment assembly or analytic loop closure approaches. In all cases, the enumerative SWA method either reaches atomic accuracy or exposes flaws in Rosetta’s high-resolution energy function, suggesting that the approach is ready for more rigorous tests. Over the last year, we have therefore helped organize and participated in blind de novo modeling trials on RNAs with previously unsolved 3D structures. For a few cases, chemical mapping and crystallographic data have become available, and we report high accuracy de novo modeling in at least two non-canonical motifs.

 

Title:
Bacterial small RNAs in regulatory networks

Speaker:
Susan Gottesman, National Cancer Institute, NIH


Abstract:
Bacteria such as E. coli contain on the order of 100 small regulatory RNAs. A large number of these regulate gene expression by pairing with target mRNAs to activate or repress gene expression; expression of the sRNAs are themselves subject to stringent regulation of their transcription. One challenge has been to identify all the targets of a given sRNA, although both experimental and computational methods continue to improve. In an alternative approach, we have developed rapid methods to query the pairing sRNAs for their effects on a given target. The combined outcome of experiments in our lab and others demonstrates an important role for sRNAs in connecting transcriptional networks, in feedback regulation of networks, and in mediating multiple regulatory inputs to many targets.

 

Title:

Folding Algorithms for RNAs with Pseudoknots

Speaker:
Peter Stadler, Boston College

Abstract:
A large variety of dynamics programming algorithms for RNA structures with pseudoknots have been proposed that differ dramatically from one another in the classes of structures considered. Mostly, these are motivated by considerations of algorithmic tractability. An alternative is the use of the natural topological classification of RNA structures in terms of irreducible components that are embeddable in surfaces of fixed genus. For genus-1 structures, this adds four additional building blocks to the conventional secondary structures.
With a single exception the resulting class of structures encompasses all known pseudoknotted structured. A corresponding unambiguous multiple context free grammar provides an efficient dynamic programming approach for energy minimization, partition function, and stochastic sampling. The topology-based approach is not only appealing from a theoretical point of view: it admits a parametrization of pseudoknot penalties that depends on topological complexity, which increases sensitivity and positive predictive value for base pairs by 10-20%.

Reidys CM, Huang FWD, Andersen JE, Penner RC, Stadler PF, Nebel ME
Topology and prediction of RNA pseudoknots. Bioinformatics 27: 1076-1085 (2011)

 

 

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Special Session 4: ELIXIR
Organizer(s):
Janet Thornton, European Bioinformatics Institute, United Kingdom

Date:   Monday, July 18
Start Time:  2:30 p.m. - 4:25 p.m.
Room:  Hall F2
 
Description: The mission of ELIXIR is to build a sustainable European infrastructure for biological information supporting life science research and its translation to:
  • medicine,
  • the environment,
  • the bioindustries, and
  • society

ELIXIR has completed a three year, European wide consultation involving academic and industrial users, data providers and international collaborators, including three stakeholders meetings, two surveys, and fourteen work packages.

ELIXIR will be a distributed infrastructure arranged as a hub and nodes, with the hub at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK.

The ELIXIR Steering Committee recently issued a Request for Suggestions for ELIXIR nodes, seeking input from organisations that are interested in hosting one of its ‘nodes’, in order to help shape ELIXIRs construction. Organisations wishing to contribute their input were requested to consider how they might contribute: data resources; bio-computing capacity; infrastructure for data integration; and services for the research community, including training and standards development.

The infrastructure is currently moving forward towards construction.
 
The ELIXIR special session will comprise:

2:30 p.m. - 2:55 p.m. Building ELIXIR presented by Janet Thornton (ELIXIR Project Coordinator) to introduce the audience to ELIXIR and the latest developments towards its construction

3:00 p.m. - 3:25 p.m. Two short presentations on:
'ELIXIR and the other ESFRI BMS Projects' presented by ELIXIR Project Manager, Andrew Lyall
and
'ELIXIR and Industry' presented by Dominic Clark, EBI Industry Programme Manager.
 
3:30 p.m. - 3:55 p.m. A panel session during which representatives from the ELIXIR Steering Committee will talk about how their country is working towards a pan European infrastructure and how ELIXIR has fostered the construction of an internal network within their country.
 
 
Chaired by: Janet Thornton (ELIXIR Project Coordinator)
Panellists: 

Anna Tramontano (University of Rome) representing Italy
Alfonso Valencia (Spanish National Cancer Research Centre- CNIO) representing Spain
Søren Brunak (Technical University of Denmark- DTU) representing Denmark
Bengt Persson (Linköping University) representing Sweden
Tim Hubbard (Wellcome Trust Sanger Institute) representing the UK

Time will be allowed after each presentation and panel session for discussion.
4:00 p.m. - 4:25 p.m. Panel Continues
 
Website: www.elixir-europe.org
 

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Special Session 5: Bioinformatics for Synthetic Biology: Scaling to Complex Biological Systems
Organizer(s):
C. Forbes Dewey, Jr., Massachusetts Institute of Technology, Cambridge, United States
Richard I. Kitney, Imperial College, London, United Kingdom
 
Date:   Tuesday, July 19
Start Time:  10:45 a.m. - 12:40 p.m.
Room:  Hall F2
 
Description:
Synthetic Biology is an emerging discipline that learns from natural biological systems and attempts to construct novel living devices that are based on biological principles. These constructs are self-replicating systems that have special functions. Making ethanol from switchgrass would be an example. Many of the constructs resemble electrical circuit elements such as and/nor gates, adders and multipliers, and feedback loops, so one can conceive of crating “living” entities that have complex decision capabilities as well as useful functions.
 
This Special Session will be devoted to exploring the role of bioinformatics in synthetic biology. One of the key concepts driving current research is the ability to combine multiple synthetic biological “parts” to achieve complex goals. With the publication and curation of these synthetic biology constructs, one can create a database of Standard Biological Parts. If the curation includes computable descriptions (e.g. ODEs that include known rate constants written in an accepted machine-readable format such as SBML), then one could predict the complex behavior of collections of these modules working as a single entity.
 
Presentations (in presentation order):
  1. Richard I. Kitney. Systematic design challenges in synthetic biology.
  2. Ron Weiss. Synthetic biology: from parts to modules to therapeutic systems.
  3. Christopher Voigt. Refactoring complex gene clusters in bacteria.
  4. C. Forbes Dewey, Jr. Managing the "BRICKS" of synthetic biology.
 
Abstract - Systematic design challenges in synthetic biology.

The paper will discuss the systematic design approach to synthetic biology. Key elements of this approach are the design cycle and the use of modularity. The paper will examine these principles in relation to two examples: biological logic gate design and a biosensor for urinary track infection.

 
Abstract - Synthetic biology: from parts to modules to therapeutic systems.
Synthetic biology is revolutionizing how we conceptualize and approach the engineering of biological systems. Recent advances in the field are allowing us to expand beyond the construction and analysis of small gene networks towards the implementation of complex multicellular systems with a variety of applications. In this talk I will describe our integrated computational / experimental approach to engineering complex behavior in living systems ranging from bacteria to stem cells. In our research, we appropriate design principles from electrical engineering and other established fields. These principles include abstraction, standardization, modularity, and computer aided design. But we also spend considerable effort towards understanding what makes synthetic biology different from all other existing engineering disciplines and discovering new design and construction rules that are effective for this unique discipline. We will briefly describe the implementation of genetic circuits and modules with finely-tuned digital and analog behavior and the use of artificial cell-cell communication to coordinate the behavior of cell populations. The first system to be presented is an RNAi-based logic circuit that can detect and destroy specific cancer cells based on their microRNA expression profiles. We will also discuss preliminary experimental results for obtaining precise spatiotemporal control over stem cell differentiation for tissue engineering applications. We will conclude by discussing the design and preliminary results for creating an artificial tissue homeostasis system where genetically engineered stem cells maintain indefinitely a desired level of pancreatic beta cells despite attacks by the autoimmune response, relevant for diabetes.
 
Abstract - Managing the "BRICKS" of synthetic biology.
One of the most exciting opportunities in synthetic biology is to assemble individual biological parts to achieve new functionality. Because the behavior of each part is, in general, highly nonlinear, simple methods of combination will not be productive. We examine current efforts to define the semantics of the “BRICKS” (Clotho, SBOL, MIRIAM, DICOM) and what is required of the underlying mathematical models that carry the quantitative information on temporal behavior.
 

Special Sessions

ISMB/ECCB 2011 features Special Session presentations throughout the conference July 17 - July 19. Special Sessions have the purpose of introducing the scientific community to relevant scientific issues and topics that are typically not within the focus of the conference. Preliminary program information on Special Sessions is noted below.
(Schedules subject to change)


Special Session 1: BioLINK: Integration across Genomics and Medicine
Special Session 2: Insights & outlook for individual genome interpretation: lessons from the Critical Assessment of Genome Interpretation
Special Session 3: RNA structure: from genomes to nanotechnology
Special Session 4: ELIXIR
Special Session 5: Bioinformatics for Synthetic Biology

 

Special Session 1: BioLINK: Integration across Genomics and Medicine
Organizer(s):
Christian Blaschke, Bioalma, Madrid, Spain
Lynette Hirschman, Mitre, Bedford, United States
Hagit Shatkay, University of Delaware, United States
Alfonso Valencia, Spanish National Cancer Research Centre, Madrid, Spain

Date:
Sunday, July 17
Start Time: 10:45 a.m. – 12:40 p.m.

 

Special Session 2: Insights & outlook for individual genome interpretation: lessons from the Critical Assessment of Genome Interpretation
Organizer(s):
John Moult, Baltimore, University of Maryland, United States
Susanna Repo, University of California, Berkeley, United States
Steven E. Brenner, University of California, Berkeley, United States

Date: Sunday, July 17
Start Time: 2:30 p.m. – 4:25 p.m.
Room: Hall F2
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Special Session 3: RNA structure: from genomes to nanotechnology
Organizer(s):
Peter Clote, Boston College, United States
Ivo L. Hofacker, University of Vienna, Austria
David Mathews, Rochester Medical Center, New York, United States
Peter Schuster, Professor emeritus, University of Vienna, Austria

Date: Monday, July 18
Start Time: 10:45 a.m. – 12:40 p.m.
Room: Hall F2

 

Special Session 4: ELIXIR
Organizer(s):
Janet Thornton, European Bioinformatics Institute, United Kingdom

Date: Monday, July 18
Start Time: 2:30 p.m. – 4:25 p.m.
Room: Hall F2
Special Session 5: Bioinformatics for Synthetic Biology
Organizer(s):
C. Forbes Dewey, Jr., Massachusetts Institute of Technology, Cambridge, United States
Richard I. Kitney, Imperial College, London, United Kingdom

Date: Tuesday, July 19
Start Time: 10:45 a.m. – 12:40 p.m.
Room: Hall F2
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