Lunch and Learn Workshop
ISMB introduces Lunch and Learn Workshops. These luncheon events are hosted by select conference sponsors - the workshops are 75 minutes in length and include a hosted lunch. Participants must pre-register with the workshop hosts. Instructions are included below on how to participate.
The Appistry Pipeline Challenge: Rewarding Researchers for Translating NGS Data into Clinical Action
Presented By:
Presenter: Brett McCann, Director of Services, Appistry, Inc.
Special Talks - ISMB 2014
Attention Conference Presenters - please review the Speaker Information Page available here
Presenter: Lynn Kamerlin
Room: 302
Date/Time: Sunday, July 13 at 11:30 a.m. - 11:55 p.m.
Session Chair: Bonnie Berger
The advent of the first enzyme structures in the 1960s, coupled to increasing computer power at the time, marked a turning point for computational enzymology. Specifically, starting in 1970, a number of different QM+MM and QM/MM approaches were introduced by Warshel and coworkers to facilitate the description of reactions in enzymes. This and molecular dynamics simulations of biological reactions (that also started with Warshel’s work), as well as the development of classical force fields, mark the emergence of multiscale models for chemical reactivity, that allowed us to begin to directly translate structural information into an energetic picture, to better understand enzyme function. In my view the most effective direction to address this problem has been the Warshel’s 1980s “empirical valence bond” approach. Despite its seemingly theoretical simplicity, the empirical valence bond approach remains one of the most powerful tools to understand chemical reactivity in biological systems even today. This talk will explore the theoretical basis and historical background for this approach, and illustrate its application to a number of the most challenging problems in computational enzymology. Additionally, the unimaginable gains in computational power of recent decades have allowed for ever more complex systems to be addressed. Therefore, this talk will conclude by discussing the power of the EVB approach to address 21st Century challenges such as enzyme design, understanding protein evolution, and addressing chemical reactivity in even such big biomolecular systems as GTP hydrolysis on the ribosome.
Presenter: Roland Dunbrack
Room: 302
Date/Time: Sunday, July 13, 12:00 p.m. - 12:25 p.m.
Session Chair: Bonnie Berger
In September of 1981, as a freshman at Harvard College, my first class on my first day of college was Martin’s Chemistry 10 course. Over the next four months, Martin proceeded to teach the outline of his influential textbook Atoms and Molecules to freshmen in what was the upper-level intro freshman chemistry course (the other was Chemistry 5 taught by Leonard Nash, who Martin had taken his intro course in chemistry from in 1947). Martin started with the quantum mechanical model of a particle in a box, then one-electron atoms, two-electron atoms, many electron atoms, the hydrogen molecule, other diatomics, triatomics, and the H+H2 reaction. The last lecture of the course he showed a movie of the one of the first molecular dynamics simulations of a protein structure, BPTI. I was astonished that this was possible, and I was hooked by the prospect of being able to understand so much of biology with theoretical and empirical chemistry and physics. I was able to work for him on quantum mechanical treatments of polyenes as an undergraduate and after finally learning some biochemistry at Cambridge after graduating from Harvard in 1985, returned to Harvard for a PhD in biophysics split between Martin and Jack Strominger in the Biochemistry Department. My work in grad school and ever since has been on the statistical end of things, but the motivation as was often the case in Martin’s work, was to solve a biological problem – initially the structure prediction of the many variants of HLA Class I proteins whose first structure was solved in 1987 by Don Wiley and Jack Strominger. I proposed and developed the backbone-dependent rotamer library as a statistical way of solving the side-chain conformation prediction problem for HLA proteins and proteins in general. It remains a central component of many if not most structure prediction and protein design programs. From Martin I learned how important it is to interpret and understand the statistical results in terms of the underlying physical forces. Just as important, I learned how to write up our work in sufficient detail that it can be replicated. I can still hear his voice in my head when I am writing papers, asking me to fill in some important detail to make everything crystal clear and reproducible. For better or worse, I still tend to write long papers because of this. In this talk, I will review our work on statistical functions of the Ramachandran map variables – density estimates, classification functions, and finally regression functions on the Ramachandran variables. Our recent regressions of bond angles of the main chain and side chains in very high-resolution structures (better than 1.0 Å) have identified aspects of current potentials that accurately reflect the high-resolution structures and areas for further improvement – indicating that some physical properties of proteins are not yet accurately modeled by current empirical force fields used in CHARMM and other programs.
Industry Posters - ISMB 2014
Presenting author: Ming Li, Personalis, United States
Additional authors:
Stephen Chervitz, Personalis, United States
Daniel Newburger, Personalis, United States
Sarah Garcia, Personalis, United States
Gemma Chandratillake, Personalis, United States
Michael Clark, Personalis, United States
Nan Leng, Personalis, United States
Jason Harris, Personalis, United States
Mark Pratt, Personalis, United States
Michael Snyder, Personalis, United States
John West, Personalis, United States
Richard Chen, Personalis, United States
Presenting author: Sivakumar Gowrisankar, Novartis Institutes for BioMedical Research, United States
Additional authors:
Zachary Zwirko, Novartis Institutes for BioMedical Research, United States
Vera Ruda, Novartis Institutes for BioMedical Research, United States
Yanqun Wang, Novartis Institutes for BioMedical Research, United States
Oleg Iartchouk, Novartis Institutes for BioMedical Research, United States
Presenting author: Michael Markie, F1000Research, United Kingdom
Presenting author: Nickolay Khazanov, Thermo Fisher Scientific, United States
Additional authors:
Sean Eddy, Thermo Fisher Scientific, United States
Marry Ellen, Thermo Fisher Scientific, United States
Jia Li, Thermo Fisher Scientific, United States
Mark Tomilo, Thermo Fisher Scientific, United States
Dinesh Cyanam, Thermo Fisher Scientific, United States
Armand Bankhead, Thermo Fisher Scientific, United States
Sarah Anstead, Thermo Fisher Scientific, United States
Nikki Bonnevich, Thermo Fisher Scientific, United States
Becky Steck, Thermo Fisher Scientific, United States
Peter Wyngaard, Thermo Fisher Scientific, United States
Seth Sadis Thermo Fisher Scientific, United States
Emma Bowden Thermo Fisher Scientific, United States
Bryan Johnson Thermo Fisher Scientific, United States
Dan Rhodes Thermo Fisher Scientific, United States
Analysis of 8,000 cancer exomes from the Oncomine® Knowledge Base to identify NFE2L2 pathway as a novel therapeutic opportunity in multiple cancer types.
Birds of a Feather (BoF) - ISMB 2014
Sunday, July 13
BOF: Open Source Communities with Impact, Leader: Manuel Corpas (Room 302)
BOF: BioFabric BoF: (nodes == lines) -> !hairballs, Leader: Bill Longabaugh (Room 313)
Tuesday, July 15
BoF: Bioinformatics Curriculum Guidelines, Leader: Lonnie Welch (Room 302)
BoF: Career Development for Women in Science, Leader: Lucia Peixoto (Room 304)
BoF: Critical Assessment of Function Annotation followup, Leader: Iddo Friedberg (Room 306)
Topic: Open Source Communities with Impact
Leader: Manuel Corpas
Affililiation: The Genome Analysis Centre
Date: Sunday July 13, 2014 12:45 p.m. - 1:45 p.m.
Room: 302
Description:
Many bioinformatics initiatives rely heavily on distributed communities of scientists and developers. What makes these communities successful? How can we harness their energy to develop scientific impact? While a compelling vision for the project is critical, effective open source communities must be able to cope with the diverse needs and demands of its members. Understanding the dynamics of remote collaborative interactions between community members is key to its success. In this BoF we will dissect the social engineering factors influencing the impact of biologically-inspired open source communities. Specifically we will focus on (i) the benefits/motivations for bioinformaticians participating in open collaborative projects and (ii) the features of higher and lower-impact communities in our field.
Topic: BioFabric BoF: (nodes == lines) -> !hairballs
Leader:Bill Longabaugh
Affililiation: Institute for Systems Biology
Date: Sunday July 13, 2014 12:45 p.m. - 1:45 p.m.
Room: 313
Description:
BioFabric (www.BioFabric.org) is a new network visualization tool that represents nodes as lines instead of as points, which creates highly organized, unambiguous, and scalable node-link diagrams. This BoF will provide users, potential users, and just the nodes-as-lines-curious to explore and discuss how BioFabric can help you to visualize your network data.
Topic: Bioinformatics Curriculum Guidelines (An Open Forum of the Curriculum Task Force of the ISCB Education Committee)
Leader: Lonnie Welch
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Affililiation: Ohio University
Date: Tuesday July 15, 2014 12:45 p.m. - 1:45 p.m.
Room: 302
Description:
The Curriculum Task Force of the ISCB Education Committee will hold an open forum to discuss its recent report “Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies” (see PLOS Computational Biology, March 2014). The discussion will focus on implementation and refinement of the guidelines.
Topic: Career Development for Women in Science
Leader: Lucia Peixoto
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Affililiation: University of Pennsylvania
Date: Tuesday July 15, 2014 12:45 p.m. - 1:45 p.m.
Room: 304
Description:
For many decades, an increasing number of women have obtained science doctoral degrees, however, women, continue to be significantly underrepresented in almost all leadership positions. While the degree of underrepresentation varies among disciplines, women's advancement to senior professorial ranks and leadership roles is an issue in all fields. Our computational biology research community is young and growing, and thus has an opportunity to set new standards in unbiased leadership, promotion, and recognition of accomplishments. Toward this, we will discuss the current state of implicit bias in hiring and promotion practices in science and outline strategies to increase career success, job satisfaction and work-life balance regardless of gender.
- Understanding Implicit Bias. Terry Gaasterland, UCSD
- Increasing your chances of success:
* What makes a job candidate stand out. Perspectives from young group leaders and the people who hire them.
Yana Bromberg, Rutgers.
* What is an "Individualized Career Development Plan" (IDP) and why it is important to have one. Michael Robinson, CHOP.
*Success factors beyond science: Jill Mesirov (BROAD), Fran Lewitter (MIT), Pankaj Agarwal (GSK)
- Open discussion
Topic: Critical Assessment of Function Annotation followup
Leader: Iddo Friedberg
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Affililiation: The Genome Analysis Centre
Date: Tuesday July 15, 2014 12:45 p.m. - 1:45 p.m.
Room: 306
Description:
Fewer than 2% of protein sequences are annotated manually, and fewer than 1% by experiments. With the advent of the $1000 genome, the analysis typically costs over $50,000. The Critical Assessment of Function Annotation (CAFA) is an ongoing effort to assess and improve computational function prediction methods. CAFA 2014 was highly successful, engaging 50 groups from 20 countries. We are looking to engage more people in the next CAFA as predictors, assessors and judges. This is a great opportunity to join a large international effort and learn about cutting-edge technologies which are used in gene and genome annotation. Funding opportunities will also be discussed, with a program officer from the National Science Foundation.
Institute for Systems Biology
ISMB 2014 - High School Teacher Workshop
Starts: Friday July 11, 2014 9am to 3pm Eastern
Location: The Hynes Convention Center in Boston
Registration has closed please contact Nadine at This email address is being protected from spambots. You need JavaScript enabled to view it. if you have any questions.
ISCB High School Teacher Workshop
Friday July 11, 2014
9am to 3pm Eastern
The Hynes Convention Center in Boston
The International Society for Computational Biology (ISCB) is hosting a hands-on workshop this July. This workshop will be taught by Dr. Fran Lewitter, Founding Director of Bioinformatics and Research Computing at Whitehead Institute and Dr. David Form, biology teacher at Nashoba Region High School. Laptops will be provided for the workshop.
The workshop will include bioinformatics activities that can be used in your classroom to help students learn biological principles. Topics include BLAST and other resources available at NCBI (the National Center for Biotechnology Information).
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Laptops will be provided for the workshop.
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There is no charge to teachers for this workshop.