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

Recruiters

The Jackson Laboratory
https://www.jax.org/Jackson Laborator

The Jackson Laboratory is recruiting outstanding Postdoctoral Associates for our expanding research campuses in Bar Harbor, Maine, and Farmington, Conn. Join our team and contribute to our important mission of discovering precise genomic solutions for disease and empowering the global biomedical community in our shared quest to improve human health.

University of Nebraska at Omaha
http://www.ist.unomaha.eduUniversity of Nebraska at Omaha

The University of Nebraska at Omaha is Nebraska's metropolitan university.



Duke University
https://www.genome.duke.edu/gcb-academy Duke University

Duke University is looking for an exceptional computational biologist to join an interdisciplinary team of biologists, clinicians, bioinformaticians, and software engineers working together to identify the genetic basis of cancer. Join our team to develop a career where your work will impact medicine and to be at the forefront of the big data revolution!



Bioinformatics and Computational Biology at Iowa State University
http://www.bcb.iastate.eduBioinformatics and Computational Biology @ ISU

The BCB Graduate Program offers interdisciplinary PhD training at the intersections of Biological, Computing and Information Sciences. More than 70 nationally and internationally known faculty - biologists, computer scientists, mathematicians, statisticians, and physicists - participate in a wide range of collaborative research projects. BCB’s 100+ alumni have achieved exceptional outcomes.

Sylvester Comprehensive Cancer Center at University of Miami, Miller School of Medicine
http://sylvester.org/University of Miami, Miller School of Medicine

Sylvester Comprehensive Cancer Center, University of Miami UHealth System, serves as the hub for cancer-related research, diagnosis, and treatment. Sylvester discover, develop and deliver therapies leading to better outcomes, providing the next generation of cancer clinical care. Sylvester has transformed cancer research and treatment in South Florida and beyond.

Sequence-Structure Moonlight Hackathon
New Times and Extended Deadlines!

July 8 - 11, 2016
Room: "Asia 3"

In the evenings of July 8th to of July 10th (after regular programming - nightly schedule), NCBI and RCSB PDB will assist ISCB in hosting a sequence-structure hackathon focused on integrating protein structure information and viewers with genomic sequence and variants, pharmacogenomic binding, and improve web based tools to visualize, annotate and share sequence and structure information. This event is for students, postdocs and investigators or other researchers already engaged in the use of javascript based viewers for protein structure visualization and/or genome/gene/protein sequence browsers. The event is open to anyone selected for the hackathon, and registered for the ISMB 2016 meeting. Those coming for the SIGs only can also join the hackathon for a nominal fee of $100 for ISCB members and $150 for nonmembers. For those who want to code all day and night the hackathon rooms will be open around the clock.

Working groups of 5-6 individuals will be formed into five or six teams. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. The potential subjects for this iteration are presenting data to and from JavaScript-viewable protein structures, simplified structure diagrams, a digital notebook for structural biologists, and pharmacogenomic association in conserved binding sites*.

Please see the application for specific team projects.

* Some of the projects will build on existing APIs feeding data to or extracting data from viewers, so not all applicants need a working knowledge of JavaScript viewers per se. For example, there is an opportunity to interface existing applications and libraries using any programming language with the Macromolecule Transmission Format (MMTF, http://mmtf.rcsb.org) for ultrafast access, parsing, and processing of PDB structures.

Organization

After a brief organizational session, teams will spend three evenings analyzing a challenging set of scientific problems related to a group of datasets. Participants will analyze and combine datasets in order to work on these problems.

Datasets

Datasets will come from the public repositories housed at the NCBI, PDB and elsewhere.

Products

All pipelines and other scripts, software and programs generated in this course will be added to a public GitHub repository designed for that purpose (github.com/NCBI-Hackathons). A manuscript outlining the design and usage of the software tools constructed by each team will be submitted to an appropriate journal.

Application

To apply, complete this form (approximately 10 minutes to complete). Applications are due June 10th, 2016 by 5 pm ET. Participants will be selected from a pool of applicants based on the experience and motivation they provide on the form. Prior participants and applicants are especially encouraged to re-apply. The first round of accepted applicants will be notified on June 13th by noon ET, and have until June 15th at noon to confirm their participation. If you confirm, please make sure it is highly likely you can attend, as confirming and not attending bars other data scientists from attending this event. We understand this hackathon is going on during an information-dense scientific meeting, so for regular ISMB meeting attendees, the hackathon sessions will be in the evening as seen in the nightly schedule. Please include a regularly used email address, in case there are follow-up questions.

Note: Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python) is necessary to be successful in this event. Knowledge of JavaScript will be particularly helpful in this event. Applicants must be willing to commit to all three evenings of the event. A small number of travel awards are available for the hackathon and the meeting. Awards for things like most prolific code development will be given at the ISCB awards ceremony on Tuesday!

For ISMB meeting attendees not participating to SIG meetings, please note that you will need to arrive on Saturday for the first Hackathon evening.

Please contact This email address is being protected from spambots. You need JavaScript enabled to view it. with any questions

Generously support by

Travel Fellowships

Travel funding is available for students and post docs. Funds are limited and will be distributed based on need. Selected participants will receive instructions on how to apply for travel fellowships in June. Travel funding awards will not cover the entire participant’s cost – maximum of $500 per award.

ISMB Exhibitor Rules & Regulations

International Society for Computational Biology (ISCB) – Exhibitor Rules and Regulations (last updated March 7, 2016)

The Exhibit Application must be electronically signed by an authorized representative of the exhibiting company. This signature will reflect that the authorized representative has read and agrees to the terms specified below. ISCB reserves the right to dismiss any Exhibitor who does not adhere to the rules and regulations published here and in the Exhibitor Service Kit.

ISCB reserves the right to interpret these regulations as it deems proper and/or necessary to ensure the success of the Exhibition and to further the educational purposes of the event. Your participation/attendance in or at this event means you, the Exhibitor, agree to comply with all ISCB Rules and Regulations, which are in effect at the time Exhibitor Move-in begins.

Presentation of Products or Services

The purpose of the ISMB exhibit program is to further the education of or assist scientists working in the field of computational biology. The exhibits must be of an educational or service nature. They must emphasize instruments; products or services for use in teaching and research; books or other publications in relevant scientific fields; or scientific research findings in those areas of science represented at the meeting. All claims regarding products and services should be truthful and accurate. Unwarranted disparagements or unfair comparisons of a competitor’s product or services are not permitted.

ISCB reserves the right, in its sole discretion, to accept or deny applications for exhibit space and to allocate space among Exhibitors. In the case of a denied application, all monies collected by ISCB will be refunded to the applicant.

Space Assignment

Assignment of space will be made on a first-come, first-served basis and must be completed via the online Exhibitor sign-up form available at: https://www.iscb.org/cms_addon/conferences/ismb2016/sponsors/index.php

Whenever possible, Exhibitor’s space requests will be honored, but the final arrangements will be determined by Exhibit Management in a way that produces the most advantageous grouping of the exhibits. ISCB shall have no liability if the space location assigned is not as requested or if space is sold out.

A 50-word description of products and/or services to be displayed in the booths must be submitted. This information will be published in the meeting program, provided that the application and description meet with ISCB approval and are received no later than May 30, 2016. If the description is not provided by the deadline date, only the name, address (as it appears on the contract), and booth number will be printed in the meeting program.

General Conduct of Exhibits

ISCB reserves the right to impose limitations on noise levels and on any other method of operation that becomes objectionable.

Exhibitors agree to abide by the installation and dismantle times set by ISCB and to have at least one person staffing their booths during published exhibition hours. All exhibitors must complete their booth installation within the designated set-up times. Failure to comply may result in additional late set-up charges. Exhibitors who vacate or dismantle their booths prior to the published exhibition closing time without permission of the show manager may be assessed a fine equal to one half the booth fee and will forfeit any booth selection for the following year.

Location Relative to Other Exhibits

Exhibitors may use the Exhibit Application to designate their preference to be located near other companies or their wish to not be adjacent to or opposite designated companies. These requests will be honored to the extent possible in conjunction with assignment priorities and requests for specific locations on the floor.

Distribution of Giveaways

Exhibitors will be permitted to distribute appropriate promotional materials and approved related items from their exhibit booth only. Exhibitors may not distribute materials outside their booth (hotels, Convention Center lobby area, etc.) without permission. In keeping with the educational purpose of the exhibit program, giveaways must conform to acceptable, legal, and professional standards. ISCB reserves the right to deny distribution of materials they deem inappropriate.

GENERAL INFORMATION

Exhibit Space Rental

All booths are approximately 8 feet x 10 feet unless stated or marked otherwise on the floor plan or in the exhibitor prospectus or contract and can be combined to make larger booths. Each booth will consist of: Each 8' x 10' booth will be set with 8' high BLUE back drape, 3' high WHITE side dividers, (1) 6'
WHITE draped table, (2) side chairs, (1) wastebasket, and a 7" x 44" identification sign.

Exhibit space must be paid in full within 30 days of receiving invoice, after which space can be resold. Exhibit fees cover only those items described in the prospectus, website page, or written communication from ISCB. Any other booth furnishings and/or equipment must be contracted through the official ISCB General Service Contractor as indicated in the Exhibitor Service Kit.

In the event that no representative of an exhibiting organization has arrived on-site to claim its space or freight within 90 minutes of the published event opening, ISCB has the right to resell or relocate the exhibit space. Any booth not set up by the last two hours of Exhibitor Move-in may be force-built at the Exhibitor’s expense or relocated at the discretion of ISCB.

During the Exhibitor Move-in/Out, the Exhibit Hall is deemed a “construction zone” by FREEMAN CORPORATION and, as such, prohibits exhibitors from wearing open-toed shoes of any kind in the Exhibit Hall. This regulation will be strictly enforced for the safety of all.

Cancellation or Reduction of Exhibit Space

Exhibitor’s decision to cancel or reduce space must be made in writing. The effective date of space cancellation or reduction will be the date the written notice is received by ISCB. In the event of a cancellation or reduction in space the following applies:

A full refund less US$100 administration fee if cancellation received prior to March 20, 2016. 50% refund if cancellation received between March 21, 2016 and May 22, 2015. No refund after May 22, 2016.

All cancellations or reduction of space include the forfeiture of all exhibitor badges that were originally allocated with the booth space.

Subleasing

Subleasing, assignment, or sharing the whole or any part of exhibit space is not permitted. Two or more companies may not share the same space. Exhibitors agree to limit the service and/or materials displayed in their exhibit area to those supplied or provided by the Exhibitor, with the exception that other proprietary equipment may be used solely for the purpose of demonstrating the materials or services of the exhibitor.

Registration of Exhibitors

Exhibitors will receive one (1) complimentary conference registration, three (3) complimentary Exhibit Hall-only badges for company personnel for each booth space reserved. Additional Exhibit Hall-only badges can be purchased for $50 each. It is the responsibility of the authorized individual signing the application for space to inform all company personnel of the rules and regulations contained in this brochure. Exhibit Hall-only badges will not allow admission to scientific sessions.

BOOTH DESIGN AND USE OF EXHIBIT SPACE

All exhibits must fit within the confines of their assigned space so as not to impede traffic flow, infringe on the space of other exhibitors, create any trip hazards, or violate the emergency exit routes or access to emergency equipment set forth by the fire marshall. The exhibit aisles will be carpeted. Exhibitors are required to cover their allotted floor space by either providing their own carpet or renting carpet from the General Services Contractor. If the Exhibitor provides their own carpet it must be one color and be clean. Exhibits Manager reserves the right to force carpet (at Exhibitor’s expense) upon exhibitors that have no floor covering or whose covering does not meet acceptable standards.

Standard In-Line Booths

The standard booth size is 8 feet x 10 feet unless stated or marked otherwise on the floor plan or in the Exhibitor Prospectus or contract. The maximum height of 8 feet is allowed only in the rear half of the booth space, with a 8 feet height restriction imposed on all materials in the remaining space forward to the aisle.

Multiple Standard Booths

In an exhibit that contains 3 or more linear booths (30 feet or more), the interior booths are permitted to contain display material with a maximum of 8 feet in height which must be confined to that area of the Exhibitor’s space which is 8 feet from an adjoining booth. Sufficient “see-through” area must be provided to avoid blocking the view of adjacent exhibits. The end booths of such an exhibit must conform to the Standard Booth restrictions. Hanging signs are not permitted. No exhibit may span an aisle by using roofing.

Exposed, unfinished sides of exhibit backgrounds must be draped to present an attractive appearance. If such draping is not ordered, the contractor, with the approval of the Exhibits Manager, will install it and charge the Exhibitor.

Island Booths

An island booth is a unit bordered on four sides by aisles. All materials and activities must be contained within Exhibitor’s designated booth space. All display material is restricted to 8 feet in height, and a sufficient “see-through” or “walk-through” area of 40% visibility per side must be provided to avoid blocking the view of adjacent exhibits. Models or to-scale drawings of exhibits must be submitted in advance to Exhibit Management for approval. Island booths will be measured and may not exceed the 8 feet height limitation. Hanging signs as part of booth structure are permitted but must not exceed the 8 feet height restriction as measured from the top of the sign to the floor.

Enclosed/Covered Booths

Exhibit space that incorporates enclosed or covered areas must be protected by an audible smoke detector. This includes storage closets built into the exhibit. Each covered or enclosed area must display a charged fire extinguisher with a minimum rating of 2A, 20BC (or conform to the locality code).

End Cap Booths

An End Cap Booth is a booth that has open sides on three aisles. An End Cap Booth must not exceed the height restrictions as noted in Island Booths.

Aisles

Aisles are the leased property of ISCB. No Exhibitor will be permitted to block aisles or otherwise impede proper flow of traffic throughout the entire show. All demonstrations must take place within Exhibitor’s designated booth space.

Fire Code Regulations

Federal, state, and city laws will be strictly observed. All drapes, curtains, table coverings, skirts, carpet, or any material used in exhibits must be flame retardant. Wiring must comply with fire department and underwriters’ rules. Hall capacity will be monitored. Fire hose cabinets, fire extinguishers, sprinklers, fire exit doors, route of egress, and any other fire safety device or facility must not be hidden, obstructed, or otherwise disturbed. Crates, packing materials, wooden boxes, or other highly combustible materials may not be stored in exhibit halls, meeting rooms, or fire-exit areas. Materials not in compliance with the regulations will be considered trash and subject to disposal. Passenger elevators and escalators may not be used for freight, including hand trucks, floats, and similar equipment.

Security

ISCB will contract reputable security guards during the course of the annual meeting. The duties of the guards will be to protect the general exhibit against fire and other catastrophes as well as to provide access control to the exhibit floor. Neither ISCB, the convention center, hotels, nor the owners or leasers of the exhibit venue will assume any responsibility for Exhibitor’s personal property. It is strongly urged that exhibitors maintain awareness of any expensive, revenue-generating, irreplaceable (within the timeframe of the exhibition), or proprietary product contained within their booth. Exhibitor will have the option of engaging security services if desired for exclusive booth coverage.

Liability

Exhibitor assumes all responsibility and hereby agrees to protect, indemnify, defend, and hold harmless ISCB and its officers, employees, and agents; the Convention Center Dublin and its employees and agents; and Freeman Companies against all claims, losses, and damages to persons or property, governmental charges, or fines, and attorney’s fees arising out of or caused by Exhibitor’s installation, removal, maintenance, occupancy, or use of the exhibiting premises or a part thereof, excluding such liability caused by the sole negligence of the parties referred to above. In addition, Exhibitor acknowledges that ISCB, its agents, the Convention Center Dublin, or Freeman Companies do not maintain insurance covering the Exhibitor’s property and that it is the sole responsibility of the Exhibitor to obtain business interruption and property damage insurance covering such losses by the Exhibitor.

The Exhibitor shall be liable to the host facility and/ or ISCB for any damage to the building and/or the furniture and fixtures contained therein which shall occur through acts or omissions of the exhibitor.

Cancellation of Meeting and Exhibit

It is mutually agreed that in the event ISMB is cancelled due to acts of God, war, strikes, government regulation or advisory (including travel restrictions by the government or World Health Organization), civil disturbance, terrorism, or threats of terror- ism in and Ireland or the United Kingdom as substantiated by governmental warnings or advisory notices, curtailment of transportation, epidemics, disaster, fire, earthquakes, hurricanes, unseasonable extreme inclement weather, shortages or disruption of the electrical power supply causing blackouts or rolling blackouts in Dublin, Ireland, or any other comparable conditions or circumstances occurring either in the location of the ISMB meeting or in the countries/states of origin of at least 30 percent of the attendees or along their routes of travel, making it commercially impracticable, illegal, or impossible to hold ISMB, the Application and Contract for exhibit space will be terminated. In such an event, neither party shall be liable to the other for delay or failure to perform its obligations, except there shall be a prorated reduction of any fees payable or otherwise due under this agreement and/or refund of any deposits paid.

Insurance

Exhibitor acknowledges that ISCB does not maintain and is not responsible for obtaining insurance covering Exhibitor’s property. Exhibitors are urged to take out a portal-to-portal rider available at a nominal cost on their own insurance policy protecting them against loss through theft, fire, damage, etc.

SERVICES AND OFFICIAL CONTRACTOR

Details for labor, furniture, rental displays, lead retrieval, utilities, etc., will be included in the Exhibitor Service Kit.

Service Kits

Exhibitor Service Kits (links) will be distributed via e-mail in April 2016. Exhibitors are encouraged to take advantage of cost reductions offered by most contractors for advance orders. Many services cost substantially more when ordered on-site.

Please address all communications to:

Steven Leard
ISMB Conference Director
Tel: +1 780-414-1663
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

ISMB 2016 Industry Sessions

Attention Conference Presenters - please review the Speaker Information Page available here.

Computational Opportunities and Challenges from Leading Companies in Industrial Biotechnology (IB)

Room: Northern Hemisphere E3/E4 Tuesday, July 12 from 10:10 am - 12:40 pm

Organizer(s):

Jean-Francois Tomb
ISCB Industry Advisory Council

Speaker(s):

Bastien Chevreux, Principle Scientist Bioinformatics, DSM Nutritional Products, United States
David Estell, DuPont Fellow - Genencor Fellow, DuPont Industrial Biosciences, United States
Sascha Losko, Head of Product Management, Biomax Informatics AG, Planegg, Germany
Karl J Sanford, Genencor and DuPont Fellow, DuPont Industrial Biosciences, United States
Amoolya Singh, Senior Scientist & Group Lead, Amyris, United States

Presentation Overview:

The outstanding success of biotechnology is based on our ability to extract and harness knowledge about genomes, biological systems and complex cell functions, and on the remarkable progress achieved in adjacent fields such as high throughput screens, reading and writing of biological polymers, process engineering, fermentation and large scale manufacturing processes, and the application of advanced computational techniques and IT solutions to catalogue, search and mine patent and scientific literature, and interpret the products of omics technologies and synthetic biology.

The goal of the industry session is to provide the ISCB community with first-hand knowledge of the computational opportunities and challenges from leading companies in Industrial Biotechnology (IB). We have invited representatives of IB companies who span the spectrum of the Biotechnology Enterprise as illustrated below.

Industrial biotechnology has a long history. From the ancient Egyptians who produced wine and bread to the first antibiotic produced in China ~ 500 BC to the more recent, 100 years-old, processes for the production of compounds such as citric, acetic and lactic acids or the use of proteases in detergents, biotechnology has been a constant companion of human innovation.

From these early days, the industry has grown significantly. The use of biotechnological processes in the production of modern goods has exponentially increased. Today, large industrial sectors utilize biotechnology as production platforms e.g. pharmaceuticals (drugs), healthcare (vitamins) and personal care (hair coloring), household goods (soaps and detergents), energy (bio-fuels), plastics (bio-degradable), electronics (sensors), textiles (leather), and agriculture (agro-chemicals). Through biotechnology solutions we are meeting global grand challenges for sustainable industrial production, food security, human health and the mitigation of environmental pollution and climate change.

Biotechnology is a vital and emerging part of global economies.

“No other sector holds the promise to enhance quality of life, productivity and environmental sustainability through innovation like biotechnology, while also benefitting Europe’s economy and research base” with these words, Carlo Incerti, Chief Medical Officer, Genzyme Corporation and Chairman of EuropaBio, opened the 3rd EuropaBio event on the Benefits of Biotechnology. Brussels, 23 June 2015.

“While not immune to the economic crisis and resulting recession, the bioscience industry weathered difficult economic times better than most industries, and is on course to regain its previous high employment levels. Indeed, the promise of bioscience-based solutions to global grand challenges … provides an optimistic picture for the biosciences as a key economic development engine in the U.S.” Report: Battelle/BIO State Bioscience Jobs, Investments and Innovation 2014.

Agenda

10:10am - 11:10am
Introduction to Industrial Biotechnology: Effective Strategies for Protein Engineering and Economical Large Scale Protein Production.

David Estell, DuPont Fellow - Genencor Fellow, DuPont Industrial Biosciences, United States

Most of the literature and academic work in Biotechnology is centered around high value pharmaceutical markets. These markets have long product lead times, relatively high price points of $8,000 per gram for protein products, and low product volumes (< 1,000 Kg per year.) Protein products sold into industrial markets have short product cycles (6-18 months), low price points (<$10 per gram) and require volumes in excess of 10,000 Kg per year. Due to these differences, extremely rapid and efficient computational tools are required to address Industrial Biotechnology needs.

Bioinformatics in the Biotech Industry – Tales from the Trenches

Bastien Chevreux, Principle Scientist Bioinformatics, DSM Nutritional Products, United States

While the skills needed by bioinformaticians in industrial biotechnology R&D overlap with those in publicly funded research, drastic differences in rather minor boundary conditions such as time and money can lead to pretty interesting differences in methodologies and approaches when it comes to solving problems with computational biology. This talk will recount some of the challenges encountered while working on the bioinformatics side of R&D projects in one the world's leading suppliers of vitamins, carotenoids, nutritional lipids and other ingredients to the feed, food, pharmaceutical and personal care industries … and how this ultimately affects the daily life of hundreds of millions of people. Examples and “lessons learned” will range from everyday user support over routine mining of large biological data sets to lead generation in ground-breaking pathway optimization research.

Computational Biology Challenges at an Industrial Biotech

Amoolya Singh, Senior Scientist & Group Lead, Amyris, United States

Amyris has developed a high-throughput genetic engineering platform for designing and building custom microbes to serve as living catalysts. Using an industrial scale fermentation process, our microbes convert renewable sugars into a wide variety of low cost, high value target molecules, including medicines, commodity and specialty chemicals. Amyris' R&D efforts span rational & random design and construction of microbial strains, high-throughput screening and analytical chemistry, fermentation at multiple scales, and genotype/phenotype data mining. Every aspect of this work is facilitated and accelerated by quantitative science and software & hardware automation. In this talk, I will outline the computational biology challenges inherent in (a) elucidating biochemical pathways (b) designing and building microbial strains (c) designing rigorous combinatorial experiments to generate reproducible data with high signal-to-noise (d) analyzing giga- to tera-bytes of complex, time-varying phenotypic data (d) learning from these data to rapidly drive the next design cycle. To meet these challenges, we use a range of innovations including genotype specification languages and high-level functional ontologies of parts and pathways; metabolic and mathematical models; machine learning algorithms; process logic and workflow versioning tools; statistical process control and design of experiments.


Coffee Break (11:10 - 11:40 am)


11:40am - 12:40pm
Beyond Silos: Knowledge Management as the Key to Operational Excellence — the BioXM System, a Universal Framework

Sascha Losko, Head of Product Management, Biomax Informatics AG, Planegg, Germany

In recent years, knowledge management systems and semantic technologies have become standard components of large-scale enterprise software infrastructures — with applications ranging from research, discovery and development all the way to operations. Process optimization and manufacturing greatly benefit from a managed “knowledge/feedback loop”. In this talk, Biomax presents their premier knowledge management platform, the BioXM system, as used early on by industry partners in synthetic biology.

Cost-effective DNA sequencing and de novo DNA synthesis have facilitated the emergence and rapid development of synthetic biology. The development of DNA assembly standards, publicly available part registries for sharing bioparts, and computer-aided design (CAD) tools have been instrumental in accelerating discovery. Applications of synthetic biology include renewable energy sources and biofuels, industrial enzymes, biosensors, drugs, vaccines and antibodies, bio-based chemicals, plastics, textiles and other raw materials, as well as food production.

The BioXM Knowledge Management system is “putting it all together,” enabling life scientists to visualize, study, create and alter highly complex pathways and DNA sequences in their genomic context. This allows efficiently building and characterizing parts repositories with respect to sequence information, part function and performance, and using these repositories to help design biological systems targeting the desired functionality. In essence, the BioXM system allows researchers to fully leverage a “design → build → test → learn” iterative approach to create improved biological systems.

Scaling up of Renewable Chemicals

Karl Sanford*, Gopal Chotani, Nathan Danielson and James A Zahnb
*DuPont Fellow - Genencor Fellow, DuPont Industrial Biosciences, United States

This presentation will review progress in the scale-up and commercialization of chemicals produced using bio-manufacturing processes. Bio based products are growing at 3-4% globally and in the U.S. alone generate over $120 billion in sales in spite of low petroleum prices and unexpected difficulties in the conversion of laboratory successes to commercialization successes. Key success factors, the importance of pilot plant work, integration of unit operations, regulatory requirements and a road map for the future will be discussed.

Q&A - Panel Discussion

Transportation

A convenient and affordable transfer between Orlando International Airport and your hotel. (Does not apply to the Orlando Sanford International Airport) Discount cannot be combined with any other discounts, special offers or promotional codes.


Instructions
  • You can book online! To receive your online discount, please go to www.mears.com, click on the “Book Orlando Shuttle Now” box then enter the code 518550079 in the “Promo Code” box provided in the lower left corner.
  • Upon your arrival at Orlando International Airport, proceed to one of the Mears Motor Shuttle ticket counters located on LEVEL 1 and present this coupon to receive your ticket. You MUST present a hard copy of this coupon or the online confirmation upon check-in at the Mears ticket counter.
  • After redeeming your coupon for a roundtrip ticket, present your ticket to the Mears Customer Service Representative located on LEVEL 1 curbside next to the crosswalk.
  • For questions, please call our toll free number at 1-800-759-5219 or locally at 407-423-5566.
  • To schedule your return transfer to the Orlando International Airport please call at least 24 hours prior to your scheduled flight time.
  • Plan to allow three hours prior to your flight time for your transfer to the airport.

Workshop 03 (WK03): Bioinfo-core Workshop

Attention Conference Presenters - please review the Speaker Information Page available here.

Monday, July 11, 2:00 pm – 4:30pm

Organizers:

Charlie Whittaker, The Koch Institute at MIT, Cambridge, United States
Jian-Liang (Jason) Li, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States
Madelaine Gogol, Stowers Institute, Kansas City, United States

Presentation Overview:

The workshop will address "The practical experience of big data and big compute". Members of core facilities will share their experience and insights via presentation and panel discussion.

Part A: Big Data

Speaker: Yury Bukhman, Great Lakes Bioenergy Research Center
Time: 2:00 pm – 2:15 pm

Presentation Overview:

The Computational Biology Core of the Great Lakes Bioenergy Research Center supports mostly academic labs at the University of Wisconsin, Michigan State University and other universities. With a variety of experiment types, they are challenged to manage and analyze disparate data and metadata in a diverse academic environment. Details of these data challenges and solutions will be discussed.


Speaker: Alberto Riva, University of Florida
Time:2:15 pm – 2:30 pm

Presentation Overview

The Bioinformatics Core of the ICBR provides bioinformatics services to the large and diverse scientific community of the University of Florida. Routine handling of projects covering a vast spectrum of biological and biomedical research requires a flexible and powerful data infrastructure. Implementation details of a software development environment (Actor) for reliable, reusable, reproducible analysis pipelines will be discussed, as well as insights on managing big data projects in a core setting.


Speaker: Big Data Panel
Time: 2:30 pm – 3:00 pm

Moderator: Madelaine Gogol, Stowers Institute for Medical Research
Panel Speaker: Yury Bukhman, Great Lakes Bioenergy Research Center
Panel Speaker: Alberto Riva, University of Florida
Panel Speaker: Hua Li, Stowers Institute for Medical Research
Panel Speaker: Jyothi Thimmapuram, Purdue University

The presenters, panelists, and attendees will explore practical experience with “big data” as well as use of public datasets in a panel discussion. Topics may include accuracy of annotation, trust of data, raw versus processed, data validation, and QC.


Coffee Break (3:00-3:30 pm)


Part B: Big Compute

Speaker: Sergi Sayols Puig, Institute of Molecular Biology Mainz
Time: 3:30 pm – 3:45 pm

Presentation Overview

With a variety of computing infrastructures available, building robust, transferable pipelines can increase utilization of compute resources. NGS analysis pipelines implemented as docker containers and deployed on a variety of compute platforms – (cluster, supercomputer, or workstation) will be discussed.


Speaker: Jingzhi Zhu, The Koch Institute at MIT
Time: 3:45 pm – 4:00 pm

Experiences transitioning a Bioinformatics core from a local to a cloud-based compute solution will be discussed, including the motivation, performance, cost, and issues with deploying bioinformatics pipelines to Amazon EC2 instances.


Speaker: Big Compute Panel
Time: 4:00 pm – 4:30 pm

Moderator: Brent Richter, Partners HealthCare
Panel Speaker: Sergi Sayols Puig, Institute of Molecular Biology Mainz
Panel Speaker: Jingzhi Zhu, The Koch Institute at MIT
Panel Speaker: Sara Grimm, NIEHS
Panel Speaker: TBA

The presenters, panelists, and attendees will discuss how people manage to stay on top of compute requirements for their own sites in a panel discussion. Major hurdles to overcome and the compromises needed for success will be discussed. We may also touch on experiences with containers and portable computing.

Workshop 02 (WK02): Workshop on Education in Bioinformatics (WEB) - Exploiting Cloud and Virtual Resources for Training

Attention Conference Presenters - please review the Speaker Information Page available here.

Monday, July 11, 10:10 am – 12:40 pm
Organizer(s):
Mainá Bitar, Brazil is currently a Post-Doctorate in Brazil and has been involved with education initiatives for a few years. She has been a member of the ISMB Student Council (ISMB-SC) Education Committee and former head of its Internship Committee. In Brazil, she has been a member of the Brazilian Association on Bioinformatics and Computational Biology (AB3C) consultive committee, a member of the ISCB Education committee and also the student representative on the board of ISCB.
Michelle D. Brazas is the Program Manager for Informatics and Bio-computing at the Ontario Institute for Cancer Research. She was previously the lead for the Canadian Bioinformatics Workshops (bioinformatics.ca) and Manager of Bioinformatics Education at OICR. She is also an executive on GOBLET and a member of the ISCB Education committee.
Fran Lewitter is Founding Director of Bioinformatics and Research Computing at Whitehead Institute for Biomedical Research. The group develops materials and provides training to biologists in the Institute. In addition, Fran is a member of the ISCB board of directors and the chair of the Education committee. She is also the former Education Editor for PLOS Computational Biology (currently on the Editorial Advisory Board) and treasurer of GOBLET.
Dr. Patricia M. Palagi is the Head of Training at the SIB Swiss Institute of Bioinformatics, Switzerland, and has been involved in bioinformatics education and training for several years. In the past, she has co-organised the ISCB workshops: ECCB12, WEB13, WEB14 and WEB15. Patricia is chair of the Fund-raising committee of GOBLET and also a member of the ISCB Education committee.
Presentation Overview:

Computing in cloud-based infrastructure is becoming increasingly prevalent in bioinformatics. Popularity with numerous code repositories, forums and in particular, application distribution platforms, has grown in parallel with increased usage of the cloud for bioinformatics. The movement goes beyond virtual machines and open sharing of code. Cloud services (Amazon, Google, iPlant), or home institution settings make available full fledge analysis pipelines (tools, data storage, access to high-performance computing), scalable to any size of research project. How do bioinformatics training programs keep pace with this changing landscape? How do bioinformatics trainers use these technology resources in their own classes, while keeping the complexity and ensuing stress to a minimum, for themselves and the trainees? What are the best technology choices for a trainee and how can learning be translated from the training environment back to the lab? More importantly, can the use of cloud resources in training be used to effectively enhance bioinformatics skills?

Through a series of presentations show-casing the use of cloud-based technologies and related tools in bioinformatics training programs, this workshop aims to highlight how these technologies can be effectively used in educational environments.

This workshop will consist of three presentations on topics ranging from packaging bioinformatics software to cloud-based compute environments, and their easy and reliable use in classrooms; and it will conclude with a panel debate on the merits and pitfalls of shifting bioinformatics training programs to the cloud.

Part A: Getting the Best Training in Computational Biology in an Era of Cloud Computing and Big Data
10:10 am – 10:35 am
Speaker: Phil Bourne, National Institutes of Health, Bethesda, United Sates
Slides
Presentation Overview:

The NIH has established a data science initiative in recognition of the increasingly analytical nature of biomedical research. From the point of view of the external research community this is embodied in the Big Data to Knowledge (BD2K) initiative which has an extensive training component. This talk will outline some of the experiences and opportunities with current training programs – courses available, training modalities etc. - with particular emphasis on the use of clouds.

Part B: How to Scale Science and People Using the Cloud
10:35 am – 11:10 am
Speaker: Nirav Merchant, Director of Bio Computing, University of Arizona, Co-PI, CyVerse Collaborative (formerly iPlant Collaborative)
Slides
Presentation Overview:

Nirav Merchant will discuss the benefits (and challenges) of adapting cloud environments to education as well as research. Working within their own customized instances, an educator (faculty member, workshop instructor, a colleague) can offer learners a uniform and reproducible setting – making it easier to teach, and safe to make mistakes. As learners scale, the cloud scales with them – from learning how to use Linux on a single-cpu instance to understanding how to mix and match cloud with high-performance computing and data grid resources.


Coffee Break (11:10 - 11:40 am)


Part C: Packaging computational biology tools for broad distribution and ease-of-reuse
11:40 am – 12:05 am
Speaker: Matthew Vaughn, Director of Life Sciences Computing, Texas Advanced Computing Center, Co-PI: Cyverse, Araport, Jetstream Cloud
Slides
Presentation Overview:

A typical instance of computational biology software is composed of interpreted code, compiled binaries, shared libraries, and shell scripts, sometimes mixed in with use of web services or databases, running in the context of a complex computer operating system, atop increasingly sophisticiated physical resources. How can we expect computations to be sharable and reproducible, and how can we hope to train people to use such resources? This talk will describe how the Texas Advanced Computing Center enables distribution and use scientific software via various approaches, including Jupyter notebooks, Github repositories, computation-oriented web service APIs, virtual machine images, and container technologies such as Docker, and how these approaches complement one another for training and education.

Part D: Panel - Experience Exchange: Ideas for Exploiting the Cloud in Bioinformatics Training
12:05 pm – 12:40 pm

Moderator: Michelle Brazas, Ontario Institute for Cancer Research
Panel Speaker: Phil Bourne, National Institutes of Health
Panel Speaker: Nirav Merchant, iPlant Collaborative
Panel Speaker: Annette McGrath, Life Science Informatics, CSIRO, Australia
Panel Speaker: Matthew Vaughn, Life Sciences Computing, Texas Advanced Computing Center

Presentation Overview:

This panel session will be a forum for discussion and exchange of strategies and approaches for applying cloud technologies and tools to the bioinformatics classroom. It will also be a discussion of the gaps and pitfalls in doing so. Come share your experiences and ideas on cloud-based bioinformatics training with the panel and audience.

Exclusively for members

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

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