Leading Professional Society for Computational Biology and Bioinformatics
Connecting, Training, Empowering, Worldwide

Upcoming Conferences

A Global Community

  • ISCB Student Council

    dedicated to facilitating development for students and young researchers

  • Affiliated Groups

    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.).

  • Communities of Special Interest

    topically-focused collaborative communities
     

     

  • ISCBconnect

    open dialogue and collaboration to solve problems and identify opportunities

  • ISCB Member Directory

    connect with ISCB worldwide

  • ISCB Innovation Forum

    a unique opportunity for industry

Professional Development, Training and Education

ISCBintel and Achievements

Special Presentations

 

James Joyce's Ulysses: A Bioinformatics Perspective Tuesday, July 14, 3:30 pm – 4:30 pm

Room: Liffey Hall 2

Presenter: David B. Searls, Independent Consultant, United States

James Joyce's classic novel Ulysses is a comprehensive depiction of Dublin and its inhabitants on a single day, 16 June 1904. Audacious in its scope and literary inventiveness, it is considered by many to be the greatest novel of the 20th century, and by many others to be unreadable. Joyce's stylistic experimentation and embrace of complexity call to mind the problems and methods with which bioinformatics deals, in its approaches to life at a micro level and the scientific literature at a meta level. This talk will explore in detail these cross-currents between Joyce's masterpiece of modernism and modern bioinformatics.

 

 

Social Events

Discover Dublin – Orienteering Ice Breaker Event

Sight Walking


Friday, July 10, 2015


Event Cost: €15.00

Event sign-in: 6:30 – 7:00 p.m. at Conference Information Desk, Convention Center Dublin (Entrance Lobby)


Event begins: 7:00 p.m. Convention Center Dublin (Entrance Lobby)
 (approximately 90 minutes in length)

Auld Dubliner


Dress code: Walking or hiking shoes, appropriate outdoor gear for the weather.

 
The annual orienteering ice breaker will provide delegates with a fun-filled 90 minutes exploring one of Europe’s most beautiful cities and provides a chance to meet friends – new and old! Gain an insight into and knowledge of Dublin’s famous landmarks and hotspots and interact with Dublin’s locals – famed for their friendly and warm welcome. Ready, steady, go.
 
Format

  • Meet and Greet
  • Teams are formed and the facilitators brief the group.
  • Challenge booklets are distributed. The booklets contain questions, tasks and challenges to be completed by the groups.


Directions, maps and images within booklets will lead participants to Dublin’s most famous and interesting landmarks such as Dublin’s Castle, Trinity College, Government buildings, the Temple Bar cultural quarter, U2 sites, James Joyce sites and more.

At each of the landmarks groups will learn a fun historical anecdote and will be instructed to carry out a task or a challenge. Examples of the tasks/challenges are:

  • Discovering a notorious superstition or the location of a valuable treasure within Trinity College.
  • Answering skill-testing questions on features of historical buildings centuries old.
  • Attempting Gaelic sport maneuvers.
  • Group activity by James Joyce’s Ulysses ‘chemist’ featured within the novel or by Oscar Wilde’s childhood home.
  • Performing a U2 song by one of the band’s legendary sites or pose for a photo imitating a famous picture of the band.
  • And much more…
Street
Concert Hall


Conference Reception at the Guinness Storehouse

Monday, July 13                7:30 pm – 10:30 pm
Location: Guinness Storehouse
St. James’s Gate, Dublin 8, IrelandGuinness Storehouse
Click To download a Map

*Cost: €25.00   Includes entrance, light reception style dinner and one complimentary pint of world famous Guinness (or wine or soft drink).

Please note transportation is not provided to attend this event. The walk time from the Convention Centre Dublin is approximately 30-35 minutes. Other options include public transit or taxi.

Join conference attendees at the Historic Guinness Storehouse. Constructed between 1902 and 1904 by Arthur Guinness Son & Co. Ltd for use as a fermentation house. Standing 125 feet high, 170 feet long and 151 feet wide it is reputedly the first steel framed building in the British Isles to be built in the Chicago style. Now a Dublin landmark capturing the history of the Guinness and one of the best views in Dublin from the Gravity Bar.

*Ticket purchase available until June 26 (close of on-line registration) at: https://www.iscbconferences.org/CONFERENCES/ISMBECCB-2015/

Learn more about the historic Guinness Storehouse at http://www.guinness-storehouse.com/en/Index.aspx

Fun Facts

  • It would take 14.3 million pints to fill the giant glass atrium in the centre of the Guinness Storehouse building.
  • Gravity Bar is the highest bar in Dublin located 46 metres off the ground.
  • St. James’s Gate at the entrance to the Guinness brewery in Dublin was once the start of a pilgrimage to Compostella in Spain and pilgrims from all over Ireland used to gather on this site to start the journey to Spain.
  • 3 million pints of Guinness are brewed every day at the St James’s Gate brewery.
  • St. James’s Gate Brewery is the biggest stout export brewery in the world.
  • The St. James’s Gate Brewery is one of the most technologically advanced breweries in the world.
  • There is approximately 198 calories in a pint of Guinness - less than a pint of orange juice!
  • Guinness is the biggest selling stout in the world with 10 million glasses being sold everyday in 150 countries
  • The ancient Irish Harp symbol was firstly used as a symbol for Guinness and only later adopted by the Irish Government as the official Government symbol.

 

 

 

Ken WolfeKenneth H Wolfe (KN04)

UCD School of Medicine & Medical Science
Conway Institute
University College Dublin, Ireland

Keynote's Website

Presentation Title: Reversible DNA rearrangement as a switch for cell type in yeasts

Date/Time: Monday, July 13th, 4:40 pm - 5:40 pm

Introduction by: Des Higgins

 

 

 

 

Abstract

We usually think of the genome as a store of information that is identical in all the cells of an individual, but capable of producing different cell types by differential gene expression. A few specialized cell types break this rule, for example by VDJ recombination in immunoglobulin gene clusters or VSG surface antigen switching in trypanosomes. These developmental genomic rearrangement processes involve the deletion of some DNA, but they can occur again and again in every generation because they only happen in somatic cells. The germline DNA remains unrearranged and is inherited by the next generation. Unicellular organisms such as yeast do not have the luxury of a separate germline and soma, so any developmental DNA rearrangements must be reversible and cannot involve DNA loss. I will describe the mechanism and evolutionary origins of one such reversible process, mating-type switching in yeast species. Yeasts have 3 cell types, which are specified by physically moving the DNA of master regulatory genes, by DNA cut-and-paste or copy-and-paste mechanisms, into chromosomal contexts where they are expressed or repressed. I discuss why in some situations evolution has chosen programmed genomic DNA rearrangement as a regulatory mechanism in preference to more common alternatives such as the differential binding of transcription factors.

 

Biography

Ken Wolfe is Professor of Genomic Evolution at the Conway Institute, University College Dublin, Ireland. His research interests are on the evolution of eukaryotic genome organization, particularly in fungi. He is best known for his discovery that an ancestor of the yeast Saccharomyces cerevisiae underwent whole-genome duplication about 100 million years ago, and subsequent discoveries of whole-genome duplications during plant and vertebrate evolution. His current research is focused on the evolution of yeast chromosome structure and the evolutionary origin of the cell-type switching process.

Eileen FurlongEileen Furlong (KN03)

 

Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

Keynote's Website

Presentation Title: Genome regulation during embryonic development

Date/Time: Monday, July 13th, 9:00 am - 10:00 am

Introduction by: Janet Kelso

 

 

Abstract

Embryonic development requires the coordinated expression of genes in both a temporal- and tissue-specific manner.  This complex regulation is controlled through the binding of transcription factors (TFs) to enhancer elements, sometimes located at great distances from their target gene.  Chromatin conformation studies have shown that gene activation by remote enhancers is associated with the establishment of a chromatin loop to the promoter element.  However, the dynamics of loop formation during development, as well as their relationship to TF occupancy and chromatin state of enhancers remains poorly understood.  It is also not clear how prevalent long-range enhancer interactions are within organisms with a compact genome.

 

To resolve the interplay between chromatin loops, enhancer activity and the regulation of gene expression, we generated a high-resolution map of enhancer-promoter interactions during Drosophila embryonic development.  We applied 4C-Seq to 100 developmental enhancers, each with diverse patterns of TF occupancy and chromatin state, and measured their 3D interaction frequencies in a specific cell-type (the mesoderm) as well in the entire embryo at two stages of embryogenesis representing dramatic developmental transitions (before and during cell fate specification).  This talk will discuss these results, and how we are complementing these efforts with very high resolution Hi-C, FISH and mutagenesis at multiple stages of development.

 

Biography

Eileen Furlong received her Ph.D. at Univ. College Dublin, Ireland and did her post-doctoral research at Stanford University, California.  She has been at group leader at the European Molecular Biology Laboratory (EMBL) since Oct 2002.  Since January 2009 she is a senior scientist and Head of the Genome Biology department at EMBL, Heidelberg.  
Over the past decade, Eileen has been instrumental in developing and applying genomic approaches to multicellular developing embryos.

 

The group’s research focuses on understanding how transcriptional networks drive cell fate decisions during development.  For this purpose, her group combines genomic, genetic and computational approaches to understand (1) the general principles of how cis-regulatory elements, including enhancers, control complex patterns of temporal and spatial activity; (2) to gain an understanding of how robust developmental progression is achieved; and (3) to build predictive models of gene expression

Applied Knowledge Exchange Sessions - Saturday, July 11

 

New for 2015!  The Applied Knowledge Exchange Sessions provide interactive educational and knowledge exchange opportunities. These sessions will be held on Saturday July 11 and a participation fee applies. Registration details and fees will be posted March 23.

AKES 01: Applied Knowledge Building networks for translation: how to use DREAM challenges and the Synapse platform as a research strategy

AKES 02: Cytoscape 3 App Development: Variations on a theme -- “Hello World”

AKES 03: Bioinformatics software testing and quality assurance

AKES 04: Open-access, cloud-based, individual-level clinical trials data - sharing, dissemination and analyses

AKES 05: Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training

AKES 06: How to navigate a bioinformatics career path

 

Note:

Morning Breaks: 10:15 - 10:45
Afternoon Breaks: 3:30 - 4:00

 

AKES 01: Applied Knowledge Building networks for translation: how to use DREAM challenges and the Synapse platform as a research strategy


Time: 8:30 am – 5:30 pm (includes 2 coffee breaks and lunch break
Room: Wicklow Meeting Room 4

Overview

This session will explain the rationale behind running a DREAM Challenge, the steps involved from both sides of the process (organizers and participants), the lessons learned, and the potential uses of DREAM Challenges in education. Hands-on exercises with the Synapse platform will be featured.

Learning Objectives:

  • Understand crowdsourcing in the form of challenges as a new approach to research
  • Learn the ins and outs of planning, implementing and analyzing a DREAM Challenge
  • Get familiar with Synapse, Sage’s platform we use to run DREAM challenges
  • Get hands-on experience as an organizer and as a DREAM participant using a toy example

Dream Challenges Background

In the last ten years both academic and commercially organized crowdsourcing efforts, often called Competitions or Challenges (Read More), have been used to evaluate the validity and rigor of scientific studies while fostering open innovation. Challenges enable an unbiased, double-blinded assessment of methods. The aggregated community predictions are robust and usually more accurate than the best performing algorithms – an effect known as the wisdom of crowds. DREAM (Dialogue for Reverse Engineering Assessment and Methods) Challenges are collaborative competitions that engage diverse communities, including statistics, machine learning and computational biology, to competitively solve a specific problem in biomedicine in a fixed time period. DREAM was founded in 2006 by Gustavo Stolovitzky and Andrea Califano, and directed by Dr. Stolovitzky since then. DREAM’s distributed community of Challenge organizers has launched 32 successful Competitions, that have led to over 100 publications using DREAM data, 25 journal articles, 1 PLOS ONE collection, 2 edited books and over 1,300 citations. DREAM has attracted the participation of over 8,000 Challenge “solvers” and evolved as a powerful approach to democratize data and accelerate research.
Since 2013, DREAM has partnered with Sage Bionetworks, to co-lead a new generation of Challenges that feature complex and/or massive data sets, including clinical, genetic and imaging data, that are hosted on Synapse, Sage’s open computational platform

Computational
Tools to Define and Analyse Logical Models of Cellular Networks
where DREAM Challenges take place. Synapse allows reproducibility of the research process by providing a collaborative environment to share data, code, results, and the analysis provenance linking these research services to one another. Users can interact with these services through the Synapse web portal or analytical clients (R, python, and command line). Synapse offers features such as real-time leaderboards, provenance tracking and community forums to incentivize continuous participation and enable teams to build upon one another’s work to evolve improved predictive models. Synapse’s IRB-approved Challenge environment permits the hosting of sensitive human data for DREAM Challenges, fosters broader participation of the research community and makes the results of DREAM Challenges (models, description and source code) available as an ongoing resource for open research.

In this tutorial we will cover all aspects related to the planning and implementation of a DREAM Challenge. We will explain the diverse aspects involved in setting up a Challenge: how to secure and curate Challenge data sets, develop and evaluate the value and rigor of Challenge questions, plan for the opening and marketing of Challenges, as well as run, score, and analyze the final results. We will also describe how to participate in a DREAM Challenge and the use of DREAM Challenges for education. We will discuss which predictive approaches seem to work well, and which type of Challenges are particularly difficult to solve and why this might be so. All throughout the tutorial, we will discuss general principles, use previous Challenges as illustrative examples, and provide “toy-data” to produce hands-on exercises in challenge organisation and participation. Hands-on demonstrations will take place using Synapse.


Session Presenters

Gustavo Stolovitzky, Distinguished Research Staff Member and Director of the Translational Systems Biology and Nano-Biotechnology Program IBM Research; Adjunct Professor, Columbia University and at the Icahn School of Medicine, Mount Sinai, United States

Dr. Stolovitzky joined IBM Research in 1998 after being a postdoctoral researcher at the Center for Studies in Physics and Biology at The Rockefeller University. He received his PhD in Mechanical Engineering from Yale University (1994) and his M.Sc. in Physics from the University of Buenos Aires (1987). Dr. Stolovitzky has received Yale University’s Henry Prentiss Becton Prize award (1994), the HENAAC’s Pioneer Award for Great Minds in STEM (2013), the World Technology Awards (2013), and Master Inventor in IBM Research (2013). Dr. Stolovitzky is a Fellow of the NY Academy of Sciences, of the World Technology Network, of the American Physical Society and of the American Association for the Advancement of Sciences.
Gustavo has led many industry projects at IBM Research including the development of single molecule DNA sequencing methods (DNA Transistor Project), and the use of crowd-sourcing to improve the quality of industrial research in systems biology (IMPROVER project). He is also heavily involved in academic research. He founded and leads the DREAM Challenges. He is a co-chair of the “RECOMB/ISCB Systems and Regulatory Genomics with DREAM Challenges” conference series. His research spans from the fields of high-throughput biological-data analysis, to reverse engineering biological circuits, the mathematical modeling of biological processes and nano-biotechnology.

Julio Saez-Rodriguez, Group Leader, European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI)

Julio studied Chemical Engineering at the Universities of Oviedo and Stuttgart, and obtained his PhD at the University of Magdeburg and the Max-Planck-Institute with E. D. Gilles. After this, he was a postdoctoral fellow at Harvard Medical School with Peter Sorger and Doug Lauffenburger at M.I.T., and a Scientific Coordinator of the NIH-NIGMS Cell Decision Process Centre. Since 2010 he is a group leader at the European Bioinformatics Institute (EMBL-EBI) , with a joint appointment in the EMBL Genome Biology Unit in Heidelberg, as well as a senior fellow at Wolfson College (Cambridge). He is an affiliated member of Sage-Bionetworks and a co-organizer of the DREAM initiative to catalyze the development of methods in systems biology. His main research interest is to develop and apply computational methods to acquire a functional understanding of signaling networks and their deregulation in disease, and to apply this knowledge to develop novel therapeutics.

Pablo Meyer, Team Leader, Research Staff Member, IBM Research

Pablo Meyer received a degree in Physics from the Universidad Nacional Autonoma de Mexico, Univeriste Paris-VII and his PhD in Biology from Rockefeller University (2005) studying with live imaging the protein interactions in the Drosophila circadian clock. He studied at Columbia University the live-imaging of metabolism during sporulation in Bacillus Subtillis. In 2010 he joined the IBM Computational Biology center at IBM Research where he is a DREAM challenges director and finds himself in the intersection between modelling, data analysis and wet lab. His most recent interests are in enzyme distribution in the cell in and their link to Metabolism/Cancer via high-throughput biological-data analysis and development of new experimental techniques.

Thea Norman, Director, Strategic Development, Sage Bionetworks, United States

Dr. Norman works closely in partnership with Dr. Gustavo Stolovitzky of IBM to oversee the running of the Sage-DREAM Challenges. DREAM Challenges foster a collaborative framework for researchers to rapidly evolve predictive disease models for tough problems in biology and medicine that would otherwise take years to produce. Dr. Norman also oversees the design and development of Sage Bionetworks BRIDGE platform. Prior to joining Sage Bionetworks, Dr. Norman spent 12 years as a science, alliance and business leader at two start-up biotechnology companies (Ironwood and Ambrx). Dr. Norman is a co-inventor on seven issued patents including that for the composition of Linzess (which Dr. Norman developed), a First in Class treatment for Irritable Bowel Syndrome. Dr. Norman holds a PhD in Chemistry from the University of California, Berkeley.

Brian Bot, Senior Scientist and Community Manager, Sage Bionetworks, United States

Brian is with Sage, a not-for-profit organization dedicated to exploring open source models in the advancement of biomedical research in Seattle, Washington. Previously, Brian worked in the Department of Biomedical Statistics and Informatics at the Mayo Clinic for 7 years. He has extensive experience in working with clinical and genomic data and has a passion for exploring innovative ways to make science more open and transparent. Brian’s current work involves implementation of strategies and technologies for making complex high dimensional genomic analyses more accessible. At its heart, this work is driven to re-envision how scientists can ensure reproducibility of their research results and communicate complex genomic science to one another and to the public at large. Brian has been an invited speaker at a number of national and international events about his experience in making science more open and transparent.


Maximum Attendees: 40

Delegate Requirements:

  • The session will include a practical component, doing hands-on exercises with Synapse. Please bring your own laptop to participate in the hands-on exercises.
  • This introductory level requires no previous experience with Challenges or Synapse although experience with R/Python is useful

top

 

AKES 02: Cytoscape 3 App Development: Variations on a theme -- “Hello World”

 

Time: 8:30 am - 5:30 pm (includes 2 coffee breaks and lunch break)
Room: Wicklow Meeting Room 5

Overview:
Cytoscape's real power lies in the ecosystem of community-developed apps. The most common types of apps provide access to third-party biological databases, customize data import for domain-specific data sets, and perform custom analyses and workflows. Browse the full collection at http://apps.cytoscape.org. During this workshop, we will demonstrate how to develop apps for Cytoscape, targeting individuals who want to take advantage of the network visualization and analysis capabilities of Cytoscape and extend it for custom use cases.

Learning Objectives:

By the end of this workshop, you should be able to:

  • Navigate the complete Cytoscape API
  • Setup an app development environment and cycle
  • Start your own app development project from scratch
  • Edit and contribute to other open source Cytoscape app projects


Session Presenter: 

John "Scooter" Morris,  University of California San Francisco, United States

John "Scooter" Morris is the Executive Director of the Resource for Biocomputing, Visualization, and Informatics and an Adjunct Assistant Professor in the department of Pharmaceutical Chemistry at the University of California, San Francisco.  Before finding his home in academia, he was a Distinguished Systems Architect at Genentech, Inc., where for 19 years, he participated in the joys and trials of life in industry.  He received his Ph.D. in Medical Information Science from UCSF in 1990, and has bachelors degrees in Physics, Biology, and Computer Science from UC Irvine.  Scooter is a member of the Cytoscape core development team, and author of several Cytoscape plugins, apps, and core features.  In his "spare time" he is the Vice President for Conferences of the ACM Special Interest Group for Computers and Human Interaction (SIGCHI) and he is known to voluntarily jump off perfectly good boats near Alcatraz Island for a brisk swim to shore.


Maximum Attendees: 20

Delegate Requirements: No previous experience required

top

 

AKES 03: Bioinformatics software testing and quality assurance

 

Time:  8:30 am – 12:30 pm (includes 1 coffee break)
Room: Liffey Meeting Room 3

Overview
Bioinformatics is the application of computational, mathematical and statistical techniques to solve problems in biology and medicine. Arguably the main research focus has so far been on the computational and statistical basis of the algorithms. Surprisingly much less effort has been placed on the quality of the design and implementation of these algorithms - even though clearly correct design and implementation of the underlying algorithm is at least as important as the algorithm itself. Incorrectly computed results may lead to wrong biological conclusions, and subsequently misguide downstream experiments. This problem is especially critical if these bioinformatics tools are to be used in a translational clinical setting. For example, given a whole exome sequencing analysis pipeline for identification of sequence variants, one must have high confidence that the resulting variant calls have high sensitivity and specificity. Although true positives can be distinguished from false positives easily through external validation, it is almost impossible to systematically distinguish false negatives from the vast amount of true negatives.

By its very nature, many bioinformatics programs are developed to organise and to analyse large and complex biological datasets. Many of these programs involve (1) processing large amount of data, and (2) invoking complex processing procedures to extract useful information. In particular, due to the rapid accumulation of high-throughput datasets and the increasing focus on systems-level biological modelling, the size and complexity of bioinformatics programs are growing rapidly. This poses a great challenge in developing a good testing strategy to ensure the reliability of the design and implementation of bioinformatics algorithms. Software testing involves defining test objectives, selecting some inputs of the software under test as test cases, executing the software with these test cases, and verifying testing results. A good testing strategy should actively reveal as many faults as possible using a selected set of test cases. Practically many key questions remained unanswered: How to design good test cases? How many test cases should be used? Can we estimate the statistical confidence of the correctness of a given software pipeline? We believe introducing and adapting state-of-the-art software testing and statistical techniques in bioinformatics is a critical step in improving the quality, reproducibility, and accountability of bioinformatics tools.

Learning Objectives:
In this workshop, we aim to create an environment to engage bioinformatics software developers, managers of bioinformatics/genomic core facilities, researchers in reliability engineering and statisticians. We hope that cross pollination of these fields would yield interesting new insight and ideas that would open new research avenue related to bioinformatics quality assurance.

Organizers
Dr Joshua Ho (Victor Chang Cardiac Research Institute, Sydney, Australia)
Dr Eleni Giannoulatou (Victor Chang Cardiac Research Institute, Sydney, Australia)

Speakers

Dr. Joshua Ho, University of New South Wales, Australia

Dr Joshua Ho is Head of Bioinformatics and Systems Medicine Laboratory at the Victor Chang Cardiac Research Institute and a conjoint senior lecturer at the University of New South Wales, Australia. He was previously an Instructor in Medicine in the Division of Genetics at the Brigham and Women's Hospital and the Harvard Medical School, USA. Besides his research expertise in epigenomics and systems biology, he has a longstanding interest in adopting state-of-the-art software testing techniques to bioinformatics (Chen et al. 2009; Xie et al. 2010; Giannoulatou et al. 2014).

Dr. Christopher Yau, University of Oxford, United Kingdom

 Dr Christopher Yau is Group Leader in Genomic Medicine at the Wellcome Trust Centre for Human Genetics, University of Oxford. He was previously a Lecturer in Statistics at Imperial College London and a Medical Research Council Research Fellow in Statistics at the University of Oxford. His main contributions to genomics have been through the development of widely used statistical tools for identifying DNA copy number alterations from array- or sequencing-based studies of constitutional or cancer genomes. More recently with the Oxford Biomedical Research Centre, as part of a Wellcome Trust Healthcare Innovation Challenge Fund programme, he has contributed to the translation of these bioinformatics tools into actual clinical healthcare and practice.

Dr. Eleni Giannoulatou, University of New South Wales Australia

Dr Eleni Giannoulatou is the senior postdoctoral scientist at the Bioinformatics and Systems Medicine Lab at the Victor Chang Cardiac Research Institute and a conjoint lecturer at the University of New South Wales, Australia. She was previously a postdoctoral researcher at the Weatherall Institute of Molecular Medicine and the Wellcome Trust Centre for Human Genetics in Oxford. Her research focuses on the development and application of statistical methodologies for analysis of modern genomic datasets arising from sequencing, microarray and other high-throughput genomic technologies, with application to human genetics, genome function and evolution.

Dr. Ruth Clifford, University of Oxford, United Kingdom

Dr Ruth Clifford is a clinical research fellow in Dr Anna Schuh’s molecular genetics research group at the University of Oxford. She has a specific interest in chronic lymphocytic leukaemia and focuses on defining high-risk genomics to aid treatment selection for this patient group where she is developing whole genome sequencing approaches to identify treatment response predictors.

 

Maximum Attendees: 50

Delegate Requirements:

  • Please bring your own laptop to participate in the hands-on exercises.
  • No specific prior knowledge is required on the topic.

 top

 

AKES 04: Open-access, cloud-based, individual-level clinical trials data - sharing, dissemination and analyses

 

Time: 8:30 am – 12:30 pm (includes 1 coffee break)
Room: Wicklow Meeting Room 3

 
Overview:

Approximately 30,000 clinical trials are run each year across the world. Different market and regulatory forces are driving initiatives to publicly share individual-level data from these clinical trials. In the broader realm of advancement of science and betterment of human condition, there are several purported benefits for the sharing of clinical trial data. The scientific community or lay public can independently verify the published results of a clinical trial.  Non-availability of original research data is known to be a significant barrier towards reproducibility. There may even be opportunity to evaluate new hypotheses that were not originally formulated in the studies, either by extending the analysis of data from a clinical trial or by combining data from different clinical trials. Multi-modal measurements are generated for each participant through different stages of the clinical trial process: physical characteristics (e.g. weight, blood pressure), medical history, clinical laboratory results (e.g. hemoglobin levels), imaging results (e.g., MRI), results of mechanistic studies employing core technologies such as ELISA, microarrays, flow cytometry and next-generation sequencing. The enormity of raw individual-level clinical and high-throughput assay data provide a tremendous opportunity for bioinformaticians to advance science, and perhaps even foster new techniques in clinical informatics. In this workshop, we will discuss the reasons for data sharing and the issues surrounding it, the various ways sharing is implemented, and showcase our experience in re-analysis of clinical trials data using open immunology studies data. We will also highlight our initial work on defining a minimum information guideline for clinical trials data release.

 

The workshop will comprise of the following four sections:

  1. Responsible sharing of clinical trials data
    Discuss the global forces that are driving initiatives to publicly share individual-level clinical trials data, major issues in data-sharing such as patient privacy concerns and intellectual property rights, and the purported benefits of data sharing.
  2. Landscape of data-sharing initiatives
    Enumerate the data-sharing mechanisms that pharmaceutical companies, government institutions and private foundations have implemented, and discuss the different flavors of data access policies that these organizations are adopting. Briefly discuss recent data sharing initiatives such as clinicalstudydatarequest.com, yoda.yale.edu and projectdatasphere.org.
  3. Minimum information about a clinical trial
    Highlight the clinical trial data elements that, in our perspective, should be part of the data that is being shared, in order to realize the very purposes of data sharing. Discuss our initiative towards minimum information about a clinical trial guideline.
  4. A use-case for sharing and re-use of clinical trials data
    Introduce ImmPort that warehouses clinical trials data in all areas of immunology that is generated primarily by investigators funded by the US National Institute of Allergy and Infectious Diseases (NIAID). With nearly 100 datasets now publicly available and hundreds of downloads per month, ImmPort is an important source for raw data and protocols from clinical trials, mechanistic studies, and novel methods for cellular and molecular measurements. Showcase, via case-studies, how researchers have reused the meta-data from clinical trials to generate new hypothesis and gain biomedical insight across multiple clinical studies.

Learning Objectives:

The participants of the workshop will

  • understand the reasons for public sharing of clinical trials data, and the issues surrounding it.
  • become familiar with different data sharing initiatives and policies implemented by pharmaceutical companies, government institutions and private foundations, and
  • gain practical introduction to accessing and re-using open clinical trials data.


Session Presenters

Atul J. Butte, Chief of the Division of Systems Medicine, Stanford University School of Medicine

Atul J. Butte has been an innovative proponent of data mining of publicly available data resources, for the discovery of novel genome-phenome relationships, and for the creation of genomic data-driven nosologies. He has served on the AMIA Board of Directors and launched the first AMIA Summit on Translational Bioinformatics in 2008. He has delivered a large number of invited Keynote/Plenary talks at international conferences, hosted workshops and served as session chair in ‘Big Data’ conferences.

Ravi Shanker, Research Scientist, Stanford University School of Medicine

Ravi Shankar is a research scientist at the Stanford University School of Medicine. In the 17 years at Stanford, he has worked in the areas of automated clinical guideline-based care, annotation standards for biomedical investigations, and clinical trial management. Currently, Ravi is member of the scientific team of ImmPort, and is research staff in Dr. Atul Butte’s lab. Ravi is exploring methods to disseminate open clinical trial data in order to support cross-analysis of clinical trials and integration of clinical trial data with other open biomedical datasets. He has lead workshops on modeling and disseminating clinical trials data.

Sanchita Bhattacharya, Lead Data Scientist for ImmPort, Senior Researcher Stanford University School of Medicine

Sanchita Bhattacharya is actively involved in the area of bioinformatics for last fifteen years doing collaborative research as a computational research scientist with biologists in academia. Her research interest includes immunoinformatics with expertise in integrative analyses of multi parameter measurements, coupled with knowledge in statistical modeling and molecular biology.


Max Participants: 40

Delegate Requirements:

  • Participants will need to install a specific version of R and few R packages on their laptops – this will be provided in advance of the AKES session.

top

 

AKES 05: Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training

 

Time: 1:30 pm – 5:30 pm (includes 1 coffee)
Room: Wicklow Meeting Room 3

Overview:
Cyberinfrastructure (CI) is a powerful enabler for data-intensive biology. Although much investigation originates in organism-centered communities there are unifying similarities across types of datasets, algorithms, and overall goals. Despite these commonalities, communities often split across domains as independently-developed tools, un-shareable datasets, and un-communicated experience results in isolation and needless redundancy.  This workshop demonstrates how CI originally developed for the U.S. plant science community (via. the iPlant Collaborative project) serves all life sciences (animals, plants, microbes, etc.) by allowing communities to leverage pre-built CI solutions and develop application-specific components to a customized endpoint. More the discussing tools, broadly applicable skills and lessons learned will be emphasized along three themes:
Scaling Data: The lifecycle of data necessitates interdisciplinary collaborations and team science approaches spanning multiple departments, institutes, and even continents. We will demonstrate how the Data Store utilizes IRODS technology to make sharing of large biological datasets routine.  
Scaling Compute: Web-accessible tools and application interfaces for data analysis and management leverage federated data and consumption of resources from multiple providers such as NSF funded XSEDE, campus clusters, and commercial clouds. Communities can access an array of tools and services, and extend the CI to accommodate specific needs.

Hands-on demos will cover:
1) Discovery Environment - Web based interface to bioinformatics application and HPC using RNA-Seq tutorials as an exemplar workflow;
2) Atmosphere Cloud Compute –overview of the Atmosphere cloud, demo data visualization applications, and developer resources;
3) Science APIs - Web-based Application Programming Interfaces (APIs) to support automation and integration of tools and services in other applications and third party platforms including authentication, job management, and developer toolkit.
Scaling People: People are by definition a component of cyberinfrastructure; A discussion with panelists from several bioinformatics-related projects will focus on educational applications of CI, best practices in training, how to develop self-sustaining training efforts (through training trainers), and how collaborating with efforts such as the Software Carpentry and Data Carpentry organizations accelerate user capabilities.

Learning Objectives:

  • Understand when and why biologist should leverage cyberinfrastructure to extract maximum value from datasets, and deliver reproducible work
  • Learn how to manage the lifecycle of data (including generation, metadata management, sharing, and post-publication access)
  • Understand why all levels of users can benefit from web-platforms for data management and analysis
  • Understand to take advantage of cloud computing by recognizing its value and its limitations
  • Learn how APIs allow users to fully customize how they consume computation
  • Learn how developers can scale their users and their software
  • Understand how and why effective training and community building makes bioinformatics projects more successful
  • Learn how to develop effective training in bioinformatics

Session Presenters:

Jason Williams, Cold Spring Harbor Laboratory, New York, United States

Jason Williams is the iPlant’s Education, Outreach, and Training Lead – Based out of Cold Spring Harbor Laboratory, Jason’s background is in plant molecular biology. For iPlant, Jason organizes, manages, and instructs more than a dozen annual bioinformatics workshops, conferences, and other events. He has been instructional staff at Cold Spring Harbor Laboratory's DNA Learning Center for the past 5 years, and been research staff at Cold Spring Harbor Laboratory for 5 years prior to that. Jason is also faculty at Yeshiva University – running a science immersion course at Yeshiva University High School for Girls. Jason has collaborated with The Genome Analysis Centre (Norwich, UK) as advisor to their scientific training programs, and currently serves on the Steering Committee of the Software Carpentry Foundation as Treasurer.

John Fonner, Texas Advanced Computing Center, University of Texas, Austin, United States

John’s interest lay in applying new technologies, hardware, and paradigms to genomic and biological problems in a way that is accessible to the average bench biologist.  His Ph.D. work was in Biomedical Engineering, involving computational chemistry and binding interactions. In 2011 John joined the life sciences computing group at the Texas Advanced Computing Center and have served and led a number of projects, all centered around either developing tools and infrastructure to support life sciences research or training scientists to leverage advanced computing resources. John has been consistently involved in teaching and training for over 8 years, including university courses, 1-on-1 mentoring, consulting, workshops, and presentations. Staying on the "front lines" of teaching technology to scientists is critical to his work as domain researcher, and active programmer, and an experienced teacher.


Additional Panelist/Presenters:

Vicky Schneider: Leads 361° Scientific Training Division, The Genome Analysis Centre, Norwich, United Kingdom
David Clements: Training and Outreach Coordinator, Galaxy Project, John Hopkins University, Baltimore, United States

Maximum Attendees: 40

Delegate Requirements: No previous experience required

top

 

AKES 06: How to navigate a bioinformatics career path

 

Time: 1:30 pm – 5:30 pm (includes 1 coffee break)
Room: Liffey Meeting Room 3

 

Overview

Working with the ISCB student council, the Junior PI group and COBE COSI, this session is focused on career development. Here, we focus on training and preparing the bioinformatics professional to successfully launch and build a career. This session will be of interest to a wide audience. For students and junior PIs, you will participate in topics and practical sessions that can help build your career. For senior faculty and other professionals, it will provide ways in which you can improve skills to mentor your students and professionals building their career.

Session outline:
1:30-2:30 Improving your elevator pitch

(organised by the ISCB Student Council)

Presented By: Mick Watson, Director of ARK-Genomics, The Roslin Institute, University of Edinburgh, UK

You’ve just bumped into the person who could decide your next career move. They are about to head to their next meeting and you have two minutes to convince them that your science is worthy. Can you do it?

In this session you will learn the theory behind how to deliver a great elevator pitch. You will then get the opportunity to put this theory to the test, honing and practicing your pitch with other audience members so that the next time you hop in an elevator, you will be ready.


2:30-3:30 Being judged: grants reviewers and journal editors.
(organised by the ISCB Junior Principal Investigators Initiative)

Presented By: Dr. Peter Rodgers, Features Editor, eLife, UK
Professor Carole Goble, School of Computer Science, University of Manchester, UK

This session will help shed light on how your science might be perceived and judged. We will hear perspectives from two people who can have a strong impact on the career path of a junior principal investigator: a journal editor and a grant reviewer.

A journal editor’s perspective. How do you write a cover letter? How do you rebut a review? How do you choose the right journal? How do you deal with the press? These questions will be answered by a journal editor who will provide insight into the judgements behind the editorial process and everything around publishing a high impact paper.

A grant reviewers perspective. What are grant reviewers looking for? What makes a grant stand out? In this session, we will be provided with a reviewer's perspective on first impressions about your grant submission and what makes for a winning grant.

3:30-4:00 Coffee break

4:00-4:30 - Witness a live interview for a faculty position.
(organised by the ISCB Junior Principal Investigators Initiative)

Presented By: Associate Professor Curtis Huttenhower, Department of Biostatistics, School of Public Health, Harvard University, USA
Professor Lawrence E. Hunter, Director of the Center for Computational Biology and of the Computational Bioscience Program, University of Colorado School of Medicine, USA

Ever wondered what it is like to interview for a faculty position? In this session, you will find out! One brave soul will participate in a “mock” faculty position interview, revealing to the audience the rigors of the interview process. Following the interview, the audience will be asked to participate in a critique of both the interviewee and interviewer.


4:30-5:30 - How to plan your career but also be aware of your opportunities.
(organised the COBE COSI)

Presented By: Professor Winston Hide, Department of Neuroscience Sheffield Institute of Translational Neuroscience, University of Sheffield
Professor Nickola Mulder, Institute of Infectious Disease and Molecular Medicine, UCT Faculty of Health Sciences, South Africa
Dr Cath Brooksbank, Head of the EBI Training Programme, European Bionformatics Institute, UK

Many people - across the entire career spectrum, from students to PIs - are uncertain about the future and what they want to do next. Some are happy simply to take the next opportunity that comes their way; others like to plan. But even those who know what they want to do may find that their plans don’t always work out - the circumstances of life often get in the way, changing the course of their careers (the best-laid plans of mice and men often go astray!).

This session will feature talks from a diverse group of successful bioinformatics individuals, who will illustrate how much of their journey was planned versus how much was the work of serendipity, and will suggest elements of the journey over which you can take some measure of control. Planning tips also include topics such as “How does one learn the best way to teach?”, “How does one learn the way to manage budget, staff, a lab, etc?”, etc.

 

Organizers

Jeroen de Ridder – Assistant Professor, Delft Bioinformatics Lab, Delft University of Technology, the Netherlands

Geoff Macintyre, Cancer Research UK Cambridge Institute, University of Cambridge, United Kingdom

Venkata P. Satagopam Research Scientist, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg

Manuel Corpas, Project Leader, The Genome Analysis Centre, Norwich Research Park, Norwich, United Kingdom

Yana Bromberg, Assistant Professor, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States

 

 

Maximum Attendees: 50

Delegate Requirements:
No previous experience required

 

top

 

ISCB Overton Prize Award Keynote

 

Curtis HuttenhowerCurtis Huttenhower (KN02)

Harvard T.H. Chan School of Public Health
Broad Institute of MIT and Harvard, Cambridge
United States

Keynote's Website

Presentation Title: Understanding microbial community function and the human microbiome in health and disease

Date/Time: Sunday, July 12th, 4:40 pm - 5:40 pm

Introduction by: Bonnie Berger

 

 

Abstract

Among many surprising insights, the genomic revolution has helped us to realize that we're never alone and, in fact, barely human.  For most of our lives, we share our bodies with some ten times as many microbes as human cells.  They are resident in our gut and on nearly every body surface, and they are a normal part of human health.  Within the past decade, new "computational microscopes" have changed our understanding of the microbiome's importance in maintaining health and mitigating disease. I will discuss our computational work in moving from a "parts list" of microbial residents and their genes to understanding molecular function, metabolism, and interactions among microbes and with our own immune systems.  Many open questions remain, however, regarding the ecological assembly driving colonization in the microbiome, its biomolecular functions, the causality of microbial community activity in various diseases, and how the microbiome can be intentionally modified to improve human health.

 

Biography

Dr. Curtis Huttenhower is an Associate Professor of Computational Biology and Bioinformatics at the Harvard T. H. Chan School of Public Health and an Associate Member at the Broad Institute.  He received his Ph.D. from Princeton University in the lab of Dr. Olga Troyanskaya, where he also performed his postdoctoral research at the Lewis-Sigler Institute.  He was an analysis lead in the NIH Human Microbiome Project and currently co-leads the "HMP2" Center for Characterizing the Gut Microbial Ecosystem in Inflammatory Bowel Disease.  His lab focuses on computational methods for functional analysis of microbial communities.  This includes systems biology reconstructions integrating metagenomic, metatranscriptomic, and other microbial community 'omics, the human microbiome in autoimmune disease such as IBD, and its potential as a diagnostic tool and point of therapeutic intervention.

Among many surprising insights, the genomic revolution has helped us to realize that we're never alone and, in fact, barely human.  For most of our lives, we share our bodies with some ten times as many microbes as human cells.  They are resident in our gut and on nearly every body surface, and they are a normal part of human health.  Within the past decade, new "computational microscopes" have changed our understanding of the microbiome's importance in maintaining health and mitigating disease. I will discuss our computational work in moving from a "parts list" of microbial residents and their genes to understanding molecular function, metabolism, and interactions among microbes and with our own immune systems.  Many open questions remain, however, regarding the ecological assembly driving colonization in the microbiome, its biomolecular functions, the causality of microbial community activity in various diseases, and how the microbiome can be intentionally modified to improve human health.

Cyrus ChothiaCyrus Chothia (KN05)

MRC Laboratory of Molecular Biology, Cambridge
United Kingdom

Keynote's Website

 

Presentation Title: How lucky I have been

Date/Time: Tuesday, July 14th, 9:00 am - 10:00 am

Introduction by: Alex Bateman

 

This special award presentation for Cyrus Chothia will feature short presentations from Arthur Lesk, Steven Brenner and Julian Gough followed by a short Q&A with Cyrus Chothia

Award Presentation by: Alfonso Valencia

 

Abstract:

TBA

 

Biography:

Cyrus Chothia came to the Laboratory of Molecular Biology (LMB) in 1970, after Ph.D. research under Peter Pauling at University College London (UCL). Three years later he started his grand tour with Fred Richards at Yale, Michael Levitt at the Weizmann Intitute and Joel Janin at the Institut Pasteur. Cyrus and Michael developed the "all-a, all-b, a/b and a+b" classification of protein structures, and with Joel, he determined principles that underlie protein-protein recognition and packing of protein secondary structures.

Cyrus returned to Cambridge in 1976, attached to the LMB and UCL, and was the E.P.A. Cephalosporin Fund Senior Research Fellow of the Royal Society until 1990. He and Arthur Lesk showed that proteins adapt to mutations by changes in structure; described how distant protein sites transmit information; and showed that the sequence of immunoglobulin hypervariable regions can predict their conformation. Cyrus collaborated with Alexey Murzin, Steven Brenner and Tim Hubbard to create the SCOP database in 1995, and with Julian Gough he created the SUPERFAMILY database in 2002.

ISCB Fellows Keynote

Amos BairochAmos Bairoch (KN06)

Professor and Director, Department of Human Protein Sciences, University of Geneva; and
Group leader, Swiss Institute of Bioinformatics
Switzerland

Keynote's Website

Presentation Title: neXtProt 2015 highlights: SPARQL endpoint and biocuration efforts around the human protein variome
Date/Time: Tuesday, July 14th, 4:40 pm - 5:40 pm

Introduction by: Burkhard Rost

 

 

 Abstract

neXtProt (www.nextprot.org) allows you to efficiently query and retrieve knowledge on all human proteins. It complements the corpus of annotations from UniProtKB/Swiss-Prot with high-quality information originating from proteomics, transcriptomics and genomics technologies. Recently we have developed an advanced search engine based on RDF/SPARQL technology.

We are also soon going to integrate an in-house developed corpus of annotations relevant to the phenotypic effects of protein mutations in human diseases with an emphasis on cancers.

 

Biography

Professor of Bioinformatics and Director of the Department of Human Protein Science at the University of Geneva, Amos Bairoch is head of the CALIPHO group of the Swiss Institute of Bioinformatics. Until June 2009, Amos headed the Swiss-Prot group which develops the UniProtKB/ Swiss-Prot knowledgebase as well as PROSITE and ENZYME. He was also co-responsible for the development of ExPASy, the world’s first website dedicated to protein molecular biology. Amos Bairoch’s main work lies in the field of protein sequence analysis and the development of databases and software tools for this purpose. Currently his main activities are focused on the development of neXtProt, a web knowledge platform on human proteins. Amos Bairoch has been awarded several distinctions, among which the European Latsis Prize, the Otto Naegeli Prize and the HUPO Distinguished Achievement Award.

Exclusively for members

  • Member Discount

    ISCB Members enjoy discounts on conference registration (up to $150), journal subscriptions, book (25% off), and job center postings (free).

  • Why Belong

    Connecting, Collaborating, Training, the Lifeblood of Science. ISCB, the professional society for computational biology!

     

Supporting ISCB

Donate and Make a Difference

Giving never felt so good! Considering donating today.