COSI Track Overview

ISMB/ECCB 2017 will provide an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology, fostering fresh dialogues and perspectives to learn about and shape the future of the field. In response to the increasing interest in the activities of the ISCB’s Communities of Special Interest (COSIs) who have previously organized the Special Interest Group (SIG) meetings at ISMB, ISMB/ECCB 2017 will be organized with the active participation of the COSIs.

An overview of the COSI program content and individual COSI sites are identified below and are updated as new program information becomes available.

• 3Dsig
• Bio-Ontologies
• BioVis
• Bioinformatics Open Source Conference (BOSC)
• CAMDA
• Function
• HiTSeq
• RNA
• Network Biology (NetBio)
• Regulatory Genomics Special Interest Group Meeting (RegGenSIG)
• Computational Modeling of Biological Systems (SysMod)
• TransMed
• VarI
• Other Topics

3Dsig

This session covers the full range of research topics and applications involving structural bioinformatics/computational biology. Event/submission URL: http://www.fourwav.es/3dsig17

3DSIG is the go to event in structural bioinformatics and computational biophysics. 3DSIG is an integral part of ISMB/ECCB with two full days of keynote presentations and oral presentations chosen from the submitted abstracts creating an unique environment for the exchange ideas between keynote speakers, PIs and students at all levels. It is impossible to fully understand biological systems without understanding the 3D structure of their constituting parts and their interactions. As such the topics relevant for 3DSIG are wide and include, but are not restricted to Structure-based drug discovery including polypharmacology and network pharmacology; Structure representation, classification and prediction; Structure-based function prediction; Docking, analysis, prediction and simulation of biomolecular interactions such as protein-protein, protein-ligand and protein-nucleic-acid; Protein dynamics and disorder; Evolution studied through structures; Application of structure to systems biology; Macromolecular assemblies; Structural genomics; 3D databases and data mining; Molecular visualization; Relevant methods of structure determination particularly hybrid methods; Prediction and analysis of protein domains; Membrane protein structure analysis and prediction; The structural basis of immunology.

Bio-Ontologies

Bio-Ontologies Special Interest Group (SIG) covers the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences.

Bio-Ontologies is celebrating its 20th year as a Special Interest Group (SIG) at ISMB. It provides a vibrant environment for reporting novel methods and sharing experiences on the construction and application of ontologies in health care and the life sciences. The informal nature of the SIG offers a constructive environment to nurture discussion of innovative and scientifically sound work that range from preliminary to completed, from both young and experienced investigators alike. Bio-Ontologies participants also benefit from a strongly interdisciplinary setting, where ISMB attendees intermingle with members from American Medical Informatics Association (AMIA) and the W3C’s Healthcare and Life Sciences interest group (HCLSIG), thereby increasing impact through broader dissemination and enabling new and exceptional collaborations.

COSI submission page: http://www.bio-ontologies.org.uk

BioVis

The BioVis session aims to educate, inspire, and engage bioinformatics and biology researchers in state-of-the-art visualization research and visualization researchers in problems in biological data visualization.

The rapid adoption of data-intensive biology approaches creates enormous challenges for computational visualization techniques, which are needed to enable researchers to gain insight from their large and highly complex data sets. The goal of this session is to bring together researchers from the visualization, bioinformatics, and biology communities with the purpose of educating, inspiring, and engaging bioinformatics and biology researchers in state-of-the-art visualization research, as well as visualization researchers in problems in biological data visualization.

Biological data visualization; Visual data analysis; Visualization tools and libraries; Usability of visualization, genome and sequence data visualization; Network and pathway visualization; Multivariate data visualization; Imaging data visualization; Workflow and process visualization; Metadata visualization

For additional details on BioVis visit: http://biovis.net
To submit an abstract for BioVis see: https://easychair.org/conferences/?conf=biovis2017

Bioinformatics Open Source Conference (BOSC)

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.

Website: https://www.open-bio.org/wiki/BOSC_2017
Abstract submission info: https://www.open-bio.org/wiki/BOSC_Abstract_Submission

CAMDA

The large, complex data sets for the Critical Assessment of Massive Data Analysis (CAMDA) contest include built-in truths for calibration. In an open-ended competition, however, both seasoned researchers and cunning students push the boundaries of our field, with unexpected questions or angles of approach often bringing the most impressive advances. We thus particularly encourage extended abstract submissions by young scientists, and colleagues taking a novel approach. Travel fellowships can support attendance. The best analysis prize is awarded by the delegates in the audience. Open discussion of different approaches encourages exchange, and is complemented by keynotes of leading researchers - recently, e.g., Atul Butte and Sandrine Dudoit (Stanford), Mark Gerstein (Yale), Curtis Huttenhower (Harvard), John Quackenbush (Dana Farber Cancer Institute, Boston), Chris Sander (Memorial Sloan Kettering Cancer Center, New York), Eran Segal (Weizmann Institute, Israel), John Storey and Olga Troyanskaya (Princeton), and Terry Speed (Berkeley & WEHI).

The Critical Assessment of Massive Data Analysis (CAMDA) sessions highlight and compare the latest methods and results in an international data analysis contest, with this year's topics including: (1) a cancer data-integration challenge for 500 children patients (FDA SEQC), (2) a meta-genomics challenge comparing swabs from subway stations in multiple cities (MetaSUB), and (3) a meta-genomics signal level challenge in Oxford Nanopore 'wiggle space'.

Contest and submissions: http://contest.camda.info

Function

The mission of the Function Special Interest Group (Function-SIG) is to bring together computational biologists, experimental biologists, biocurators, and others who are dealing with the important problem of gene and gene product function prediction, to share ideas and create collaborations. The Function-SIG holds annual meetings alongside ISMB. Also, we are conducting the multi-year Critical Assessment of protein Function Annotation, or CAFA, experiment.

Website: http://biofunctionprediction.org/
Submissions: http://biofunctionprediction.org/abstract_submissions/

HiTSeq

HiTSeq is a special interest group devoted to the latest advances in computational techniques for the analysis of high-throughput sequencing (HTS) data.

Sessions will be devoted to discussing the latest advances in computational techniques for the analysis of high-throughput sequencing (HTS) datasets and will provide a forum for in-depth presentations of the methods and discussions among the academic and industry scientists working in this field. We seek contributions on any topic involving HTS data analysis including: genome assembly and haplotype phasing; transcriptome analysis; genetics and epigenetics variation; metagenomics and microbiome analysis; and new HTS platform data analysis (e.g. synthetic reads, long reads, nanopore). In addition to general sessions, we propose to have two specialized sessions to focus on current hot topics: a) long sequencing and mapping techniques, b) single cell sequencing applications, c) non-linear genome representations. Both of these topics have generated an enormous amount of interest recently.

Submission Link: https://easychair.org/conferences/?conf=hitseq2017
Website: http://hitseq.org

RNA

This session covers the full range of research topics in the field of RNA Biology, from computational and high-throughput experimental methods development to their application in different aspects of RNA processing, structure, and function.

The goal of the Computational RNA Biology session is to bring together experts in computational and experimental aspects of research in RNA Biology to cover new developments across this broad field of research. The meeting focuses on two major areas: (1) the development of computational and high-throughput experimental methods, and (2) the application of such methods to break new grounds in the study of RNA biology and disease. We aim to educate and inspire researchers in the field, novice and seasoned alike, by meshing together different aspects of Computational RNA Biology, and promoting cross-disciplinary collaborative research.

URL: http://irbgroup.org/rna-sig-17/

Network Biology (NetBio)

This session covers the full range of research topics and applications in the field of Network Biology.

The goal of the Network Biology session is to cover new developments across this important and still burgeoning field. The session will focus on two major areas: (1) the development of network-related tools and resources, and (2) the application of network analysis and visualization in the study of biology and medicine. The session will thus provide a unique interface between tool developers and users in the field of network biology. Through these complementary lenses, the session will bring into focus the current state of the field, its future promise and how to get there.

Website: http://connect.iscb.org/communities/netbio

Regulatory Genomics Special Interest Group Meeting (RegGenSIG)

Abstracts Area Chairs - RegGenSIG: This email address is being protected from spambots. You need JavaScript enabled to view it. and This email address is being protected from spambots. You need JavaScript enabled to view it.
Regulatory genomics involves the study of the genomic "control system," which determines how, when and where to activate the "blueprint" encoded in the genome. Regulatory genomics is the topic of much research activity worldwide. Since computational methods are important in the study of gene regulation, the RegGenSIG meeting focuses on bioinformatics for regulatory genomics. An important goal of the meeting is to foster a collaborative community wherein scientists convene to solve difficult research problems in all areas of computational regulatory genomics.

Website: http://tare.medisin.ntnu.no/reggen/2017/

Computational Modeling of Biological Systems (SysMod)

The Computational Modeling of Biological Systems (SysMod) aims to create a forum for systems modelers and bioinformaticians to discuss common research questions and methods. The session will focus on the conjoint use of mathematical modeling and bioinformatics to understand biological systems functions and dysfunctions. The meeting is open to the full range of methods used in systems modeling, including qualitative and quantitative modeling, dynamical and steady-state modeling, as well all applications of systems modeling including basic science, bioengineering, and medicine.

Submission Link: http://sysmod.info/SysMod_ISMB_2017:_Call_for_Abstract

TransMed

This session covers the current developments in the field of clinical and translational medicine informatics.

In this TransMed session, we will explore the current status of computational biology approaches within the field of clinical and translational medicine. Large amounts of multi-omics, imaging (medical and molecular) and clinical data can now be captured for given patient populations. This opens the debate on current state-of-the-art data infrastructures for translational medicine data integration and analysis. A variety of computational approaches are currently being used to harmonize and relate molecular data to clinical outcomes in order to better understand disease conditions. These methods also have the potential to discover biomarkers for early detection of disease, and targets for drug discovery, and to be used predictively to help to suggest personalised therapeutic strategies for patients. In this session we will bring scientists from both academia and industry to exchange knowledge and foster networking, to help in building up of the translational medicine community.

VarI

VarI-SIG session discusses the recent advances in the methodology for the annotation and analysis of genetic variants.

The VarI-SIG meeting is dedicated to the recent advances in the analysis and interpretation of the genetic variants. The meeting aims to organize a research network (VarI-COSI) facilitating the exchange of ideas and the establishment of new collaborations between researchers with different expertise. The VarI-SIG meeting is broadly divided in two sessions (“Genetic variants as markers: evolution, populations, GWAS” and “Genetic variants as effectors: function, structure, and regulation”) that encompass the four major research topics of the field:
1) Databases, data mining algorithms and visualization tools for variants analysis. 2) Methods for predicting regulatory/structural/functional impacts of SNVs. 3) Personal Genomics, GWAS studies and SNV prioritization. 4) Population genomics and phylogenetic analysis.

Website: http://varisig.biofold.org/

Other Topics

Abstracts Area Chair - Other: This email address is being protected from spambots. You need JavaScript enabled to view it., Carnegie Mellon / University of Pittsburgh, United States

Other Topics represents research areas that are not included in the above COSIs. Selected abstracts will be programmed into parallel tracks throughout the meeting. If your abstract is technical in nature, please visit the Technology Track submission portal here.

To submit to Abstracts: Other Topics go to: https://easychair.org/conferences/?conf=ismbeccb2017abstract

Industry Poster Package

For-profit organization $1,250
Not-for-profit organization $1000

Industry posters are intended to convey information about commercially available software and services.

• One poster display in industry poster section
• Poster and author listed in conference program app
• One full conference registration

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

COSI Organizer Information Page

• COSI Track Benefits
• Abstract Submission Process
  Proceedings Submission Process
  
• Poster Submission Process
• COSI Track FAQ

COSI TRACK BENEFITS

• $1000 per day (speaker honorarium or can be used to purchase additional registrations)
• Five (5) full conference complimentary registrations (name and email addresses required no later than May 15 to This email address is being protected from spambots. You need JavaScript enabled to view it.)
• Reduced fee ($475) additional registrations if needed (maximum 10 – name and email address required no later than May 15 to This email address is being protected from spambots. You need JavaScript enabled to view it.)
• $10 per delegate commissions who identifies COSI attending. This commission is calculated after the conference and may be distributed based on total average percent of attendance.
  
  • After the meeting, each COSI will receive a commission from the conference revenues for each individual that attended their track. The commission matrix will be determined by the COSI advisory board. It will be a combination of number of paid registrants that selected the COSI as their track, number of actual attendees in the session room, and a possible third criteria.
  • Reduced and complimentary registrations do not count towards COSI commission attendance numbers
• Additional $1000 for COSI who have more than 250 register for the full conference
• Un-restricted use of escrow funds to support COSI track speakers or additional events
• Full allocation of any sponsorship raised by COSI to COSI escrows

Abstract Submission Process

1. Each COSI responsible for reviewing and selecting speakers and posters. COSIs should invite reviewers for abstract and poster review by January 30, 2017.
2. To assist with duplication each COSI should add field to their submission system that requests:
   “Other COSI Submissions: Please identify any other COSIs you have submitted your research for review.”
3. Provide lists of proposed speakers to other COSI to avoid duplication. Please note a presenting author can present only one oral talk at ISMB/ECCB 2017.
4. Provide lists of submitters choosing poster option to This email address is being protected from spambots. You need JavaScript enabled to view it. (Please note submission directly to the posters website opens January 16. We are asking submitters to only submit here if not submitting an abstract to individual COSIs. The Poster Chair is Casey Greene).

* Note: CAMDA, CAFA and BioVis provide partial schedules on May 17th. Additional information provided at a later date as selection for some talks depends on performance in an assessment

Setting up EasyChair for Abstract Submission

1. To set up EasyChair you will need to apply for a new conference at www.easychair.org
   > Apply for a new conference installation AND in the "Any other information" part of the form the COSI should write: "This conference should be added to the group license of ISCB/ECCB 2017”.
2. For those submitters to the COSIs who do not receive an opportunity to present their work orally we hope they will consider presenting a poster in stead. In order to avoid having to re-submit to the ISMB/ECCB 2017 poster site we are requesting each COSI include the following field in their submission form: When adding details, include the following field
   Please consider my submission for a poster if it is not accepted for oral presentation How to add in Easychair:
   • Go to 'Administration' then 'Configure'
   • On the configure page select 'Submission Form’ then click on 'Additional fields in the submission form'
   • Once here it will show you several examples of types of questions you can add. Go to the upper right hand corner and 'Add a new field'
   • This is where you will add a checkbox with the following text: Please consider my submission for a poster if it is not accepted for oral presentation

Groups not using EasyChair are asked to include the field in their submission forms. Following your notification process we ask that you provide This email address is being protected from spambots. You need JavaScript enabled to view it. with an excel list of those indicating “yes” and their submission information. The conference organizers will then be in contact with them regarding their poster participation.

Proceedings Track Process:

1. Proceedings Chair(s)
   • Oversee the review program including managing key dates and ensuring reviews are completed for all Areas of the Proceedings Track.
   • Manage the EasyChair submission system.
   • Either reassign to appropriate areas, or arrange the review of any submissions to the category “Other”
   • Manage the proceedings selection teleconference with Area Chairs – generally 36-40 papers are selected for inclusion in the Special Issue of Bioinformatics online and are presented orally at the conference.
   • Serve as the reviewers of Conflict of Interest (COI) submissions (papers submitted by Area Chairs or the other Proceedings Chair)
   • Liaise with OUP/Bioinformatics as required
   • Write the OUP/Bioinformatics Editorial
     Example of Special Issue of Bioinformatics available at: http://bioinformatics.oxfordjournals.org/content/32/12.toc
2. Area Chair(s) (referred to as ACs)
   • Invite reviewers to participate in the review process through the EasyChair submission system (draft invite below). Papers should each receive 3 reviews. Invitations can be sent outside of EasyChair if you prefer.
   • Provide advice to reviewers as required and ensure reviewers have completed reviews by established deadlines.
   • Rank submissions selecting a list of at least the top 4 (for two-day COSI) or top 2 (for one-day COSI) to be presented in the respective session. Accepted papers that do not fit into the respective session will be presented in another session.
   • The top submissions from each COSI should be confirmed with the COSI Leaders to ensure they reflect the program goals of the COSI for presentation at the conference.
   • The top submissions from each COSI will be presented at an “all” Area Chair teleconference to review the final acceptance list of papers.
   • Area Chairs may find that submissions to their area are better suited in another area.
     1. if this is determined before the paper is reviewed the ACs should notify the Proceedings Chairs so the paper can be moved.
     2. if however, the paper has been reviewed, then determined that it would be better suited in another area, it would only be moved if the paper was deemed to be a quality/important submission (poor quality submissions reviewed would not be re-reviewed in another area).
3. Program Committee / Reviewers (referred to as the PC)
   • Review 4-6 submitted papers in their area
   • Provide comments and scoring using the EasyChair system by deadline.

Review Committee Invitation (sample)

Dear XX,
We invite you to participate as a member of the ISMB/ECCB 2017 Program committee to review proceedings manuscripts in the area of XXX. All reviewers are required to review up to 4-6 submissions (dependent upon the number received) by DATE.
Please let us know by DATE that you are able to join us as a part of the Program Committee – your contribution helps make the conference a success,
Thank you,
NAME
Area Chair, AREA

Reviewer DataBase

A list of reviewers from 2016 is attached as a reference for inviting and has been added to https://www.iscb.org/cms_addon/services/revcount/

This database is meant to help with reviewer invitations and is populated on a voluntary basis. If you invite someone — please indicate that by selecting your COSI and clicking the “Invited” checkbox. If the person subsequently accepts or declines the invitation, please access the page again to select the respective radio button. Counts are there to inform you of the current requests load on the individual you are planning to ask to review. To add another person, use the text boxes on top of the page. Note that there is not sophisticated algorithm or validation running on the back-end — if you make a mistake, there is no way to backtrack from the web-interface. At the end of review process, we will compile the list of people that have accepted review assignments for recognition on main ISMB/ECCB web-page. The list will be forwarded to the appropriate COSis for validation.

Poster Track Process

(submission details at https://www.iscb.org/ismbeccb2017/2930

1. Poster Chairs:
• Oversee the review program including managing key dates and ensuring reviews are completed for all areas of the Poster Track including early and late posters.
• Manage the EasyChair submission system.
• Review submissions in the “Other” category
• Liaise with ISCB programmer ensuring accepted posters added online including those reviewed through COSI Abstract submission sites.
• Establish and coordinate poster prize committee to review finalists for poster awards.
• Select prize winners for announcement at conference awards presentation.
2. Poster Area Chairs (COSIs):
• COSIs to identify Poster Area Chairs to This email address is being protected from spambots. You need JavaScript enabled to view it. to be included in EasyChair submission system.
• Oversee the review program within COSI area ensuring key dates are met.
• Invite reviewers to participate in the review process through the EasyChair submission system (draft invite below). (*If reviewers are known in advance to simply add them to poster COSI track)
• Rank top two (2) poster submissions for consideration of poster awards. (This should also include posters submitted as part of COSI Abstract submission process).
3. Poster Review Committee:
   Acceptable posters:
   • Does it seem possible that the poster describes some sort of scientific project?
   • Is it roughly within the domain of the COSI?
   • It must not describe a commercial product (there is a separate track for that).
   Poster award nominees:
   • All of the criteria for acceptable posters are met.
   • The abstract is well organized.
   • The research described is important for the domain of the COSI.
   • The methodological components, as can be assessed from the abstract, appear to be sound.
   • There is a conclusion that is supported by the results described in the abstract.
   • The poster highlights the diversity of the research area of the COSI.
4. Key dates:
   

   Early Posters
   January 16, 2017	Call for early posters opens
   May 15, 2017	Early posters submission deadline
   May 31, 2017	Early posters submission deadline

   Late Posters
   May 16, 2017	Call for late posters opens
   June 5, 2017	Late posters submission deadline
   June 12, 2017	Late posters submission deadline

Reviewer Invitation (draft)

Dear XX,

We invite you to participate as a member of the ISMB/ECCB 2017 Program committee to review posters. All reviewers are required to review up to 10-12 submissions (dependent upon the number received) by DATE.

Please let us know by DATE that you are able to join us as a part of the Program Committee – your contribution helps make the conference a success,

Thank you,

NAME
Area Chair, AREA

COSI Track FAQ

Q: Can COSIs invite submitters of non-accepted proceedings talks to present in our COSI Track?
A: Yes, you are welcome to invite these submitters to present an oral abstract as part of your COSI track by writing directly using the contact information provided during the submission process.

Q: Can an author present more than one oral presentation at the conference?
A: In order to provide the opportunity for as many attendees as possible to participate in the conference, only one oral talk per presenter will be accepted. In exceptional cases, speakers may be invited to present a second talk if the topics are considered sufficiently distinct. This decision will be left to the COSI committees, but we would strongly encourage you to consider inviting another group member, or selecting an equally good alternative talk. Overall, the meeting benefits from its diversity and breadth, and the organizing committee encourages the COSIs to continue work together to ensure that this is maintained.

COSI Abstract Information Sharing (Nomi Harris, BOSC)

1. Ask authors which other COSIs they’re submitting to
Add a checkbox field to your submission form to let authors indicate which, if any, other COSIs they are submitting to. In EasyChair, you do this by going to Administration -> Configure -> Additional fields in the submission form. Add a multi-checkbox field for COSIs. You then have to tediously hand-add one by one the name of each COSI (that will be shown on the form) and the internal value (that will be used to represent that field in the database).

The screenshots below show what this field will look like for submitters (pink box) and what it looks like in the EasyChair configuration interface (table with grayish cells).

2. After April 13 submission deadline, share author/COSIs spreadsheet with other COSI chairs.

EasyChair lets you export an Excel spreadsheet of all the submissions. You can export a table with author names, abstract title, and other fields such as the “COSIs” field that I suggested adding. To keep this message from getting too long, I won’t describe the process right now, but I can send another message later explaining how to do this in EasyChair.

We would then populate a shared Google spreadsheet with a tab for each COSI, and someone can prepare a combined spreadsheet that lists all authors with multiple submissions and which COSIs they submitted to. This will help the COSI chairs decide, perhaps even before the review process, which COSI each multiply-submitted abstract fits best in.

3. Decide which COSI will accept each multiply-submitted abstract.

Before notifying authors (May 10), the COSI chairs may need to negotiate about multi-submitted abstracts so that each abstract receives only one acceptance. This discussion needs to happen at least a few days before May 10 so that chairs can adjust their acceptance decisions appropriately. For example, if a good abstract was submitted to BOSC and Bio-Ontologies and it was decided that Bio-Ontologies would take it, that might leave a hole in the provisional BOSC schedule that I would need to fill (perhaps by accepting another more marginal abstract or giving another abstract a longer talk slot).

I suggest that each COSI chair have a provisional acceptance list by May 3 and that we schedule a conference call on May 5 to resolve any conflicts. That leaves a few more days for chairs to adjust their acceptance lists before sending out notifications on May 10.

ISMB/ECCB Distinguished Keynote

Zhiping Weng
Director, Program in Bioinformatics and Integrative Biology
Professor, Biochemistry and Molecular Pharmacology
University of Massachusetts Medical School
Worcester, United States

Presentation Title: ENCODE Encyclopedia: Featuring a Registry of Candidate Regulatory Elements and the Visualization Tool SCREEN for Searching Them
Time: Monday, July 24 — 8:30 am - 9:30 am
Introduction by: Yves Moreau, ISMB/ECCB 2017 Conference Co-chair
Room: Forum

Abstract:
Jill Moore, Michael Purcaro, Henry Pratt, and Zhiping Weng Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA

The Encyclopedia of DNA Elements (ENCODE) Consortium has generated thousands of genomic datasets with the goal of annotating the functional elements in the human and mouse genomes. As members of the Data Analysis Center of the Consortium, we have worked with other Consortium members to integrate such genomic datasets generated by the ENCODE and Roadmap Epigenomics Consortia to create a collection of genomic annotations termed the ENCODE Encyclopedia. The Encyclopedia has three levels. The ground level consists of annotations that are very close to the experimental data, such as DNase I hypersensitive sites (DHSs) and “peaks” of histone modifications or transcription factor occupancy. In the middle level of the Encyclopedia resides a registry of candidate regulatory elements (cREs) that are anchored on DHSs in roughly 200 human cell types and 50 mouse cell types, and further annotated with histone modifications and transcription factor occupancy. We show that the registry is accurate in identifying functional promoters and enhancers in a cell type specific manners, evaluated using functional data such as mouse transgenic assays. We also show that the registry is comprehensive—it can identify promoters and enhancers in cell types for which DNase-seq experiments have not been performed. The top level of the Encyclopedia contains chromatin state calls using semi-automated genome annotation algorithms such as Segway and ChromHMM, for those cell types that have been interrogated by a complete or near-complete set of epigenomic assays. We have developed a Web-based database and visualization tool SCREEN (Search Candidate Regulatory Elements by ENCODE). SCREEN enables users to explore candidate cREs in the Registry across hundreds of cell and tissues types and filter regions by various facets. The user can use SCREEN to compare enhancer-like elements across tissues, predict enhancer-gene interactions, visualize gene expression profiles, and annotate genetic variants. SCREEN also provides the functionality to access and download supporting data, as well as visualize regions of interest using dynamic graphs and external genome browsers.

Biography:
Zhiping Weng received her B.S. in Electrical Engineering from University of Science and Technology of China in 1992 and Ph.D. in Biomedical Engineering from Boston University in 1997. Dr. Weng is a full professor and Director of Program in Bioinformatics and Integrative Biology at University of Massachusetts Medical School. She develops and applies computational methods to study biological problems, e.g., gene regulation by transcriptional and post-transcriptional (small silencing RNA) mechanisms and protein-protein interaction. Dr. Weng is a key member of the ENCODE consortium and heads its data analysis center. She is also a member of the data analysis center of the psychENCODE consortium. Her lab performs integrative analysis on the rich genomic, epigenomic, and transcriptomic data generated by the two consortia.

Additional details available here.

Student Council Symposium 2017

The Student Council Symposium is a forum for students, post docs, and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge.

Room: Meeting Hall IV
Date: Friday, July 21
Time: 8:30 AM - 6:00 PM

Full details available at: http://symposium.iscbsc.org

ISMB/ECCB Distinguished Keynote

James Sharpe
EMBL-CRG Systems Biology Unit
Centre for Genomic Regulation (CRG)
Barcelona, Spain

Presentation Title: Dynamic computer modeling to span the scales: from molecular circuits to organogensis.
Time: Saturday, July 22 — 8:30 am - 9:30 am
Introduction by: Janet Thornton, ISMB/ECCB 2017 Conference Co-chair
Room: Forum

Abstract
The predominant emphasis of genomics, bioinformatics and computational biology is at the molecular scale, however many of the things we wish to understand occur at the macroscopic scale of organs and organisms: the development of a phenotype, the spread of a cancer, the regeneration of an organ. At the molecular scale, regulation of genes and proteins creates complex networks which control cell activities (division, migration, cell fate decisions, differentiation, and many others), with both an intracellular part (circuits of transcription factors) and an extracellular part (secreted ligands which move between cells allowing cell-cell communication, such as FGFs, WNTs, etc). The coordination of thousands of cells by this extended molecular network, leads to large-scale morphogenesis at the scale of tissues and organs. However, these large-scale tissue movements also feedback to the molecular scale: the movement of tissue regions relative to each other causes cells to receive dynamically changing concentrations of signaling molecules, and this in turn changes the activation or repression of genes and proteins.

A full understanding of this large-scale feedback between genes, cells and tissues will require multi-scale computer modeling, and we have chosen vertebrate limb development as a model system to explore this problem. Crucially, the data on gene expression and tissue movements should be both dynamic and spatial. Traditional high-throughput “omics” technologies do not preserve spatial information, and we therefore develop novel 3D imaging technologies (OPT and SPIM) to generate geometric and spatial data for the models. I will present results of this interdisciplinary modeling approach, which is gradually allowing us to tackle this complex problem.

Biography:
Originally captivated by computer programing, later at Oxford University James Sharpe saw the mystery of multicellular development as even more amazing: How the circuitry of gene regulation vaguely resembles electronic control circuits, but with a totally distributed control system (every cell containing the same genome, and thus the same circuit). He then trained as an experimental developmental biologist (PhD at NIMR London), moved to Edinburgh (MRC HGU) to start developing computer models of limb development (1997), invented a new 3D mesoscopic imaging technique called Optical Projection Tompgraphy, and in 2006 moved to the CRG (Barcelona) to pursue a systems biology approach to organogenesis - integrating experimentation, imaging and computer modeling.

Additional details available here.

ISCB 2017 Innovator Award Keynote

Aviv Regev
Broad Institute of MIT and Harvard
Cambridge, United States

http://www.hhmi.org/research/reconstruction-dynamically-rewiring-circuits-population-single-cells

Presentation Title: Reconstructing Cellular Circuits: From Cells to Tissues
Time: Friday, July 21 — 6:15 pm - 7:15 pm
Introduction by: Bonnie Berger, ISCB Vice President
Room: Forum

Abstract
Molecular circuits of multiple interacting molecules process information in cells and connect diverse cells together into the functioning ecosystem of tissues. In this talk I will describe how recent advances in single cell and spatial genomics, genetic perturbation, and analysis methods open up new opportunities for dissecting complex circuits, all inspired and driven by computation and analytics. These include reformulating problems, using new experimental strategies inspired by computational considerations, and developing new analysis algorithms to derive unprecedented impact on the cells that make up the human body, the circuits that underlie their function, and how they come together in tissues in homeostasis and disease.

Biography
AVIV REGEV, a computational and systems biologist, is a professor of biology at MIT, a Howard Hughes Medical Institute Investigator, the Chair of the Faculty and the director of the Klarman Cell Observatory and Cell Circuits Program at the Broad Institute of MIT and Harvard, and co-chair of the organizing committee for the international Human Cell Atlas project.

She studies the molecular circuitry that governs the function of mammalian cells in health and disease and has pioneered many leading experimental and computational methods for the reconstruction of circuits, including in single-cell genomics.

Regev is a recipient of the NIH Director’s Pioneer Award, a Sloan fellowship from the Sloan Foundation, the Overton Prize from the International Society for Computational Biology (ISCB), the Earl and Thressa Stadtman Scholar Award from the American Society of Biochemistry and Molecular Biology, and the ISCB Innovator Award, and she is a ISCB Fellow (2016).

Regev received her M.Sc. from Tel Aviv University, studying biology, computer science, and mathematics in the Interdisciplinary Program for the Fostering of Excellence. She received her Ph.D. in computational biology from Tel Aviv University.

ISMB/ECCB 2017 – Tutorial Program – Friday, July 21

• Tutorial AM1: Single Cell Transcriptomics (SOLD OUT)
• Tutorial AM2: Ontologies in Computational Biology (SOLD OUT)
• Tutorial AM3: 3D Genome Data Processing, Analysis, and Visualization (SOLD OUT)
• Tutorial PM4: Network Analysis in Cytoscape: Advanced Topics (SOLD OUT)
• Tutorial PM5: Prediction of Regulatory Networks from Expression and Chromatin Data (SOLD OUT)
• Tutorial PM6: Making Galaxy Work for You

ISMB/ECCB 2017 features half-day tutorial sessions on Friday, July 21, 2017 one day prior to the start of conference scientific program.

Tutorial attendees should register using the on-line registration system. Tutorial participants must be registered for the ISMB/ECCB conference to attend a tutorial. Attendees will receive a Tutorial Entry Pass (ticket) at the time they register on site. Lunch is included in the registration fee for attendees registering for two tutorials. Those attending one tutorial only have the option to purchase a lunch ticket during on-line registration.

Presenters:
Anagha Joshi, Division of Developmental Biology, Roslin Institute, University of Edinburgh, United Kingdom
Jeanette Baran-Gale, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, United Kingdom

After nearly a decade in existence, short-read bulk RNA-sequencing has decidedly gone mainstream, but new technologies keep evolving to reveal ever more intricate aspects of the transcriptional landscape of a cell. Single cell sequencing makes it possible to trace cellular differentiation in minute detail, to study cell-to-cell heterogeneity or to identify rare cell types. Being a recent and currently evolving technique, the data processing and analysis protocols are currently far from standardized. This half a day tutorial session will present recent advances in the development and application of new computational tools, resources and methods to analyze single cell RNA sequencing data highlighting the strengths and weaknesses of these techniques. We will particularly provide a hands-on activity to analyze single cell data generated by smart-seq2 and 10x platforms.

Schedule Overview

Participant Overview:
Beginner or Intermediate

The target audience are researchers who have recently started working on or plan to work in near future with single cell data (Beginner or Intermediate), as well as anyone who is working with large scale genome-wide data and wants to know more about the opportunities and challenges presented by these new data (Broad Interest).

Class Size: 30

Presenter Bios:
Anagha Joshi, Roslin Institute, University of Edinburgh, United Kingdom
Jeanette Baran-Gale, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, United Kingdom Jeanette Baran-Gale is a postdoctoral research fellow in the lab of Chris Ponting at the MRC Institute of Genetics & Molecular Medicine, University of Edinburgh. Her current research focuses on investigating the mechanisms underlying promiscuous gene expression in thymic epithelial cells using single cell RNAseq. Her past research includes high-throughput analysis of both coding and non-coding RNAs in several disease models including the estrogen response in breast cancer.

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Presenters:
Dr. Michel Dumontier, Maastricht University, Netherlands
Dr. Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia

Tutorial Overview:

Ontologies have long provided a core foundation in the organization of biomedical entities, their attributes, and their relationships. With over 500 biomedical ontologies currently available there are a number of new and exciting new opportunities emerging in using ontologies for large scale data sharing and data analysis. This tutorial will help you understand what ontologies are and how they are being used in computational biology and bioinformatics.

Schedule Overview

Participant Overview
The tutorial will be of interest to any researcher who will use or produce large structured datasets in computational biology. The tutorial will be at an introductory level, but will also describe current research directions and challenges that will be of broad interest to researchers in computational biology.

Presenter Bios:
Dr. Michel Dumontier, Maastricht University, Netherlands
Dr. Robert Hoehndorf, King Abdullah University of Science and Technology, Saudi Arabia

Presenters:
Nezar Abdennur, PhD student, MIT, United States
Nils Gehlenborg, Harvard Medical School, United States
Peter Kerpedjiev, Harvard Medical School, United States
Soo Lee, Harvard Medical School, United States
Jian Ma, Carnegie Mellon University, United States

Tutorial Overview:

Motivation: Due in large part to the explanatory power of chromosome organization in gene regulation, its association with disease and disorder as well as the unanswered questions regarding the mechanisms behind its maintenance and function, the 3D structure and function of the genome are becoming increasingly target of scientific scrutiny. With efforts such as the 4D Nucleome Project and ENCODE 4 already beginning to generate large amounts of data, the ability to analyze and visualize it will be a valuable asset to any computational biologist tasked with interpretation of experimental results.

Goals and Objectives: After the workshop participants should be able to obtain, process, analyze, and visualize 3D genome data on their own as well as to understand some of the logic, motivation and pitfalls associated with common operations such as Hi-matrix balancing and multi-resolution visualization. Specifically, our objectives include: • To introduce the theoretical concepts related to 3D genome data analysis
• To familiarize participants with the data types, analysis pipeline, and common tools for analysis and visualization of 3D genome data
• To provide a hands on experience in data analysis by walking through some common use cases of existing tools for data analysis and visualization.

Schedule Overview