ISMB 2022 Health and Safety Protocols

We encourage you to monitor this page to stay abreast of the latest updates on health and safety protocols for ISMB 2022. ISCB reserves the right to alter these protocols as appropriate at any time as its leadership continues to assess the situation. (last update: February 28, 2022)

The safety of conference participants is ISCB’s top priority, and we believe the most effective way to ensure the safety of all attendees is for them to be vaccinated and boosted if eligible and able against COVID-19. Please note that proof of vaccination will be required for all in-person conference participants prior to traveling to Madison, WI, USA.

Participants should be aware that, while ISCB will make every effort to reduce the risk of COVID-19 transmission on site, it is possible that attendees will come in contact with people in airports, hotels, and around the conference facility who could potentially carry the virus, which is why ISCB is requiring attendees to be fully vaccinated for their own safety, as well as the safety of others.

Entry into the United States (US) may require measures beyond those that are stated by ISCB to gain access to the country.  As ISCB is required to abide by US entry requirements, please be sure to consult the COVID-19 Traveler Information page of the US State Department.  Other References: US CDC International Traveler Requirement; US FDA list of accepted vaccines; Visit Madison City Information

ISCB is also required to adhere to all state and local regulations and restrictions as imposed by local governments.  You are encouraged to review the local regulations and restrictions that are in place in the city of Madison, WI, USA (https://www.cityofmadison.com/health-safety/coronavirus).

Participants of the ISMB 2022 understand that it is their responsibility to review and ensure compliance with any stated country guidelines both for coming into the US and departing the US to return to their country of origin.  Costs associated with travel are the responsibility of the participant.

References: US CDC International Traveler Requirement; US FDA list of accepted vaccines; US State Department COVID-19 Traveler Information page

For the purposes of right of entry to ISMB 2022, a person is considered fully vaccinated:

• Two weeks after receiving the second dose in a two-dose series, such as the Pfizer and Moderna vaccines; or
• Two weeks after receiving a single-dose vaccine, such as the Janssen (Johnson & Johnson) vaccine; or
• Full course of immunization with any vaccine that has been authorized by the World Health Organization (WHO). The product may be either fully authorized or authorized under an emergency use authorization or equivalent at the time of travel (see list of eligible vaccines - {https://covid19.trackvaccines.org/agency/who/} ).
• And is boosted with a booster shot if person is eligible and able

Vaccination with a vaccine that is not included on the WHO website as authorized will not be accepted.

For those unable to travel or meet the vaccination requirement, ISCB offers several virtual meeting registration options – https://www.iscb.org/ismb2022-register.

How will vaccinations be verified?

Prior to arriving on site, participants electing to attend in-person will be asked to upload proof of vaccination status during registration.  ISCB will accept any Country, Province, or State proof of vaccination image, which is to include COVID vaccine certificate or a “CLEAR health pass”. 

In addition to all attendees, all ISCB staff working at the meeting will be fully vaccinated; however, ISCB is not legally able to require local convention center staff to be vaccinated.  ISCB is working with local entities in Madison, WI, USA,  to develop on-site protocols in accordance with the Centers for Disease Control and Prevention (CDC) guidelines, including requiring all local conference facilities staff to wear masks.

Will ISCB require proof of a negative COVID test upon arrival?

While ISCB will not require proof of a negative COVID test prior to arrival onsite, ISCB, however, strongly encourages all in-person participants to test for infection prior to departing for the conference.  As testing times vary world-wide, our suggested test period is no more than 48 hours from the departure of your home.  

Entry requirements are updated often.  Be sure to check the entry requirements well in advance of your departure to the conference and return to your home country.

References: US CDC International Traveler Requirement; US FDA list of accepted vaccines; US State Department COVID-19 Traveler Information page

On-Site Safety Measures

Public health guidance on preventing the transmission of COVID-19 continues to evolve, and ISCB will base its on-site protocols on the latest guidance from the CDC in addition to local regulations in Madison, WI, USA.

We would encourage attendees to bring their own test kits and test prior to attending the meeting and at regular frequency during the meeting to reduce the risk of transmitting COVID-19. We can assist attendees who have no access to tests.  ISCB will provide the locations of local retail stores where tests can be purchased and will have a limited number of tests at the convention center for purchase by the attendee. 

Air Circulation

The Monona Terrace air ventilation and filtration systems meet the ASHRAE (American Society of Heating, Refrigerating, and Air-Conditioning Engineers) recommendations. Systems have a minimum of three (3) air exchanges per hour in a function space.  The number of exchanges is determined by how many rooms on a specific air handling unit are in use and to what air temperature we are heating or cooling the room.

For air filtration, Monona Terrace filters at a HEPA (High Efficiency Particulate Air) level, using MERV 8 pre-filters and MERV 15 final filters.

Physical Distancing

Meeting rooms will be set up to accommodate those attendees who prefer more personal space as well as those who prefer to sit closer together, even if physical distancing is not legally mandated at the time of the meeting.

Sanitization

Even though the science now shows that COVID-19 transmission is less likely to occur from touching surfaces touched by multiple persons (i.e., lecterns), staff will clean these regularly to promote healthy sanitation overall. The convention center will also have sanitization stations throughout the venue.

Protective Masks

The wearing of protective masks is required of all attendees, ISCB staff, and conference facility workers, regardless of whether or not it is required by law at the time of the meeting. Participants are welcome to bring their own mask of choice. N95 and KN95 (FFP2) masks are strongly preferred. Surgical masks are accepted but known to be less effective.  Cloth masks, gaiters, bandanas, and masks with exhalation valves will not be accepted. Masks will be provided onsite for a donation (suggested $1) should you need one.

Masks must be worn properly (covering both mouth and nose) at all times indoors, except as noted below. The indoor mask requirement applies to all spaces where in-person ISCB events are being held. Masks are not required outdoors.

Masks may be removed briefly in the following situations:

• When actively eating or drinking*, eating and drinking are prohibited within the session rooms
• When speaking at the lectern (as the distance between the speaker and audience is greater than 6 feet). Speakers should put their masks back on when not actively presenting (i.e., sitting at the head table on the dais).*
• When being photographed or interviewed on camera by registered media or ISCB staff.*

*PLEASE NOTE: Attendees should maintain a distance of at least 6 feet from others when unmasked in the above-mentioned situations

Participants who are not properly masked will be refused admittance to ISCB sessions and events and may have their badges revoked. Please see Centers for Disease Control guidance on masking.

Symptom Development While Onsite

On-site participants must agre that if they become symptomatic they will immediately get tested for COVID-19 and cease participation in the meeting and all related events. Individuals who test positive will not be permitted to continue attending the meeting in person until a negative test is produced and must follow CDC guidance on quarantine and isolation.

COVID-19 Testing

ISCB will not be providing a testing facility onsite at the conference location, Monona Terrace.  ISCB will have self-administered rapid antigen tests (supply limited, testing kits sponsored by a generous donation by Akamai) available at the registration desk for those who may wish to test during the conference.  If you are onsite and experiencing symptoms, please contact ISCB (This email address is being protected from spambots. You need JavaScript enabled to view it.); we will bring a test to your hotel.

Those wishing to be tested at a clinic or testing facility should visit Public Health Madison & Dane County for the most up-to-date information on testing options.  Many local pharmacies across Dane County, community test sites and the Public Health clinic at 2230 S. Park St. in Madison, all provide testing. Rapid drive-thru testing is available through Walgreens.

If you wish to arrange testing without traveling to a clinic or laboratory, you may consider this concierge service by Pivotal Health, https://pivotalhealth.care/locations/madison-wi/.

If your travels home require a documented laboratory result, Madison/Dane County testing facilities can be found at https://publichealthmdc.com/coronavirus/testing#testing.

You may also consider purchasing  Abbott BinaxNOW™ COVID-19 Ag Card Home Test through eMed.  Most airlines will accept this tele-health verified self-administered test. Please be sure to check with your airline prior to purchasing.  Abbott BinaxNOW™ COVID-19 Ag Card Home Test can be found at https://www.emed.com/airline-travel and other retail providers. ISCB will also have a limited supply available at the registration desk.

Complimentary testing supplies are brought to you by a generous sponsorship from Akamai. ISCB has a limited supply of rapid antigen tests and Abbott BinaxNow COVID-19 Ag Card Home Test through eMed which will be distributed complimentary to those in need (donations to support travel fellowship funds are encouraged).  Once the testing supply is depleted, we will do our best to obtain additional tests at the expense of the participant. ISCB strongly encourages participants to bring their own testing kits if they wish to test throughout the conference.

What happens if I test positive onsite?

Participants who test positive for COVID-19 onsite, must follow CDC guidance on quarantine and isolation. They will not be allowed to attend sessions in person until a negative test can be produced, although they will still have access to the virtual platform. Staff on site will be available to provide assistance to individuals who test positive via a Quarantine Support Concierge. Support will include:

• Daily wellness phone calls to check on the individual.
• Assistance with modifying hotel arrangements to extend the check-out date to the end of the quarantine period. The cost of the additional quarantine period will be the responsibility of the participant. ISCB has worked with the hotels to provide reduced hotel rates for quarantine purposes.  
• Coordination with the hotel for the contactless delivery of water, food, beverages, and housekeeping supplies, since housekeeping service will cease (food costs will be the responsibility of the participant)
• Coordination of contactless delivery of other items needed from non-hotel sources (i.e., pharmacy or grocery stores; at cost to the participant)

Quarantine Support Concierge services will be available July 8, 2022 through July 16, 2022.

Information on individuals who test positive, including the name of the individual testing positive and the session in which the individual participated, will be provided to staff overseeing the COVID-19 testing and response efforts. This will enable staff to follow up with these individuals to provide information on policies for isolating while on site, facilitate safe and comfortable quarantine arrangements, and provide information on local health care options as needed. While aggregate information about the number of positive cases will be made available to other attendees, the identity of individuals who test positive will be kept confidential.

Unfortunately, a formal contact tracing system is not available. ISCB will, however, make aggregate data available to attendees via the conference app about the number of positive cases reported at the meeting on a daily basis so they can make informed decisions about their participation. The identity of individuals who test positive will be kept strictly confidential.

COVAC GLOBAL

While ISCB is taking numerous precautions to alleviate the risk to meeting attendees, the possibility of testing positive during the meeting, and therefore needing to quarantine in place per the CDC guidelines {https://www.cdc.gov/coronavirus/2019-ncov/your-health/quarantine-isolation.html}, may factor into the decision to attend the conference. To help address these concerns, ISCB recommends COVAC GLOBAL, a leading provider of medical evacuation services, to offer in-person attendees the option to purchase its COVID-19 Evacuation and Repatriation service. For those who purchase this service in advance, COVAC GLOBAL will arrange for medical transport – via private jet – back to your home to complete your quarantine at no additional expense, should you be diagnosed with COVID-19 while at the conference.

International Attendees

International attendees should always check current travel restrictions to the U.S. on the Centers for Disease Control and Prevention (CDC) website, before planning your travel, to make sure you will be able to enter the U.S. In addition, please monitor local regulations at the origin destination to ensure that you will be able to return from the U.S.

Conference Refund Policy

ISCB understands the continued volatility of the ongoing pandemic. In the event a registered participant cannot travel due to a positive test result prior to departing for the conference, ISCB will partially refund the participants registration fee to still allow the participant access to the virtual platform.  Participants who are still unable to participate in the conference virtually may request a full refund. Full refund requests must be made prior to the start of the conference and be accompanied by positive COVID-19 testing documentation . ISCB will not accept refund requests after 6:00 PM CDT, July 10, 2022.

ISCB COVID Waiver

Upon registration to the conference, ISCB will require all in-person participants to sign the following waiver:

I understand that travel and gathering involves risk of sickness, including sickness from COVID-19. I (and on behalf of my guest(s)) waive and release ISCB and its sponsors and exhibitors, and their employees and agents, from and against claims, liabilities and expenses arising from injury, sickness or death from contraction or spread of COVID-19 or other communicable disease due to travel to or attendance at an event sponsored by ISCB.

I will take necessary precautions while at the event including, but not limited to, engaging in appropriate social distancing, wearing a mask when requested and/or required, minimize face touching, frequently washing hands and avoiding risky environments such as overcrowded bars or restaurants. I agree to not attend any ISMB event if I feel ill or had recent exposure to a COVID-19 case. This waiver and release is binding on me and my heirs and successors.

Introduced by: Janet Kelso, ISCB Treasurer; Max Planck Institute for Evolutionary Anthropology, Germany
Time: Thursday, July 14, 2022 at 8:30 AM - 9:30 AM CDT (Live Stream)
Room: Madison Ballroom ABCD (Level Four, Monona Terrace)

Presentation Title: Comprehensive identification of cancer driver mutations

Abstract

Somatic mutations are the driving force of cancer genome evolution. Given the evolutionary principles of cancer, one effective way to identify cancer genes is by tracing the signals left by the positive selection of driver mutations across tumours. Using this concept we analyze thousands of tumor genomes to generate a compendium of cancer genes across tumor types (http://www.intogen.org), and we build machine learning models inspired in evolutionary biology that effectively identify driver mutations in each gene and cancer type (http://www.intogen.org/boostdm). The results (integrated in  CancerGenomeInterpreter.org) contribute to the interpretation of tumor mutations in precision cancer medicine.

Biography

Nuria Lopez­-Bigas is an ICREA Research Professor at the Institute for Research in Biomedicine in Barcelona. She is interested in the identification of cancer driver mutations, genes and pathways across tumor types and in understanding the mutational processes leading to the accumulation of mutations in cancer cells. Her lab (http://bbglab.irbbarcelona.org) combines strong expertise in biology and bioinformatics. They are the developers of IntOGen.org, a compendium of cancer genes across cancer types, and of CGI (cancergenomeinterpreter.org), a tool to annotate cancer driver mutations and biomarkers of drug response in individual tumors. Nuria Lopez­-Bigas was elected member of the European Molecular Biology Organization (EMBO) in 2016 and Fellow of the International Society of Computational Biology (ISCB) in 2021.

Introduced by: Christine Orengo, ISCB President; University College London, United Kingdom
Time: Wednesday, July 13, 2022 at 8:45 AM - 9:45 AM CDT
Room: Madison Ballroom ABCD (Level Four, Monona Terrace)

Presentation Title: Integration, modularity and network analysis for understanding disease

Abstract

The availability of large multi-modal biological datasets invites researchers to deepen our understanding in basic science and medicine, with the goal of personalized analysis. While inquiry of each data type separately often provides insights, integrative analysis has the potential to reveal more holistic, systems-level findings. We demonstrate the power of integrated analysis in disease by developing algorithms on several levels, including subtyping based on multiple omics for the same cancer; identifying and ranking driver genes in an individual's tumor based on expression and mutation profiles; and predicting a healthy individual’s future risk of developing cancer based on data from routine periodical checkups.  Modularity and network analysis are recurring themes in our studies.

Biography

Ron Shamir (PhD, UC Berkeley 1984) is a Sackler professor of Bioinformatics in the Blavatnik School of Computer Science at Tel Aviv University. His group develops algorithms and software tools in bioinformatics for understanding the genome and human disease.

Shamir is the founder and head of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.  He has published more than 300 scientific works, including 17 books and edited volumes, and has supervised more than 60 research students.  He participated in the creation of RECOMB and of the Israeli Society of Bioinformatics and Computational Biology.  He is a recipient of the Landau Prize in Bioinformatics, the Kadar family prize for excellence in research, and a Fellow of the ISCB and the ACM. 

Introduced by: Mona Singh, Conference Co-chair; Princeton University, United States
Time: Monday July 11, 2022 at 8:45 AM - 9:45 AM CDT
Room: Madison Ballroom ABCD (Level Four, Monona Terrace)

Presentation Title: Haplotype-informed discovery of hidden genetic variants influencing human traits

Abstract

Genetic association studies have discovered hundreds of thousands of common single-nucleotide polymorphisms (SNPs) associated with human phenotypes. However, such associations have generally been difficult to interpret, often only providing hints of other nearby genetic variants that causally modify traits. In this talk, I will describe progress on ascertaining and evaluating the effects of understudied forms of genetic variation, including variable number tandem repeats (VNTRs) and copy-number variants (CNVs). This work has been powered by statistical methods that leverage haplotype-sharing among distantly related individuals in large biobank cohorts.

Biography

Po-Ru Loh leads a statistical genetics research group in the Division of Genetics at Brigham and Women's Hospital and Harvard Medical School. His lab broadly seeks to develop and apply efficient computational tools that enable exploration of genetic effects on complex traits in biobank cohorts. Originally trained as a mathematician, he developed an interest in human genetics as well as in algorithm design during his graduate studies. He and his lab have made contributions in genome-wide association analysis, haplotype phasing, and the study of inherited and somatic genomic structural variants and their effects on human health.

NIH-NSF Smart Health Program

Tuesday, July 12                                                 (10:30 AM - 12:30 PM; 2:30 PM - 3:30 PM CDT)

The purpose of the NIH-NSF interagency Smart Health program is to support the development of transformative high-risk, high-reward advances in computer and information science, engineering, mathematics, statistics, behavioral and/or cognitive research to address pressing questions in the biomedical and public health communities. Transformations hinge on scientific and engineering innovations by interdisciplinary teams that develop novel methods to intuitively and intelligently collect, sense, connect, analyze and interpret data from individuals, devices and systems to enable discovery and optimize health. Solutions to these complex biomedical or public health problems demand the formation of interdisciplinary teams that are ready to address these issues, while advancing fundamental science and engineering.

More information can be found in NSF Solicitation 21-530 and NIH Notice NOT-OD-21-011

Date: July 11-12, 2022

Location:
Liberty Room, Hilton Madison Monona Terrace
9 E Wilson St
Madison, WI, 53703
United States

Please see these important details:

Registration (required; not included with ISMB registration) at: https://broadinstitute.swoogo.com/vrs-hackathon-ismb

GitHub repo: https://github.com/ga4gh/vrs-hackathons

The Variation Representation team of the Global Alliance for Genomics and Health (GA4GH) is hosting a focused hackathon for interested members of the ISMB community to collaboratively shape and develop useful features supporting adoption of the GA4GH Variation Representation Specification (VRS). The hackathon would cover two days of focused, community-driven participation reducing barriers to the use of VRS as an emergent standard.

The goals of this workshop are to:

• Identify community-driven projects to enable use of GA4GH VRS in bioinformatics workflows, tools, and databases
• Drive engagement between the VRS core development team and the ISMB community
• Provide hands-on experience using and contributing to VRS

Schedule:

ISMB 2022 Tutorial Program

In-person Tutorials (All times CDT)

• Tutorial IP1: Gene regulatory network inference from single-cell transcriptomics data
• Tutorial IP2: A practical introduction to the design, quantification, and analysis of CRISPR genome editing data
• Tutorial IP3: Guidelines for the assessment and analysis of lrRNA-seq data for transcript identification and quantification (LRGASP challenge) - CANCELLED
• Tutorial IP4: GA4GH: An introduction to federated genomics using the GA4GH Starter Kit and real-world data platforms
• Tutorial IP5: Julia for Data Science
• Tutorial IP6: Data processing and visualization in the cloud with Terra, Dockstore, and Galaxy

Virtual Tutorials: (All times CDT) Presented through the ISMB conference platform

• Tutorial VT1: Introduction to Python programming for bioscientists
• Tutorial VT2: Building Interactive Visualizations of Genomics Data with Gosling
• Tutorial VT3: Federated Learning in Biomedicine
• Tutorial VT4: Towards Precision Medicine with Graph Representation Learning
• Tutorial VT5: Computational analysis of antibody repertoires, with applications for therapeutic discovery
• Tutorial VT6: Online tools for visualizing RNA structure

Room: E
Sunday, July 10, 11:00 am – 6:00 pm CDT

Organizer(s):
Kedar N Natarajan, Technical University of Denmark
Kyle Akers, Virginia Tech, United States
Blessy Antony, Virginia Tech, United States
Marek Prachar, University of Copenhagen, Denmark
TM Murali, Virginia Tech, United States

Single-cell transcriptomics has become the state-of-the-art for profiling cell types and states from heterogenous complex tissues, and can facilitate investigation into underlying regulatory mechanisms. The recent wealth of large single-cell RNA-sequencing (scRNA-seq) studies including atlas-scale datasets have enabled an improved appreciation of cell type complexity and underlying regulatory mechanisms. A growing suite of computational methods termed gene regulatory network (GRN) inference approaches take the input scRNA-seq data (alongside annotations), and infer activity of master regulator transcription factors with their downstream targets within single-cells. These GRN (TF-target) inference approaches integrate the upstream epigenetic and signalling cascades to provide an improved understanding of both cell type-specific and consensus (multi cell-type) TF regulation.

We will cover a GRN inference methods (TENET) and GRN benchmarking framework (BEELINE) using simulated and real scRNA-seq data through hybrid lectures and hand-on-training sessions. We will cover the principles underlying these methods, their assumptions and trade-offs. We will benchmark multiple methods, interpret results and discuss strategies for further in silico validation. The audience will be equipped with practical knowledge, essential skills to conduct GRN inference independently on their own datasets and interpret results.

Learning Objectives:
At the completion of the tutorial, participants will gain understanding into the basic concepts and recent advances in GRN inference methods for single-cell transcriptomic datasets. Four learning objectives are proposed:

1. Understand the basics principles underlying GRN inference from scRNA-seq data;
2. Understand the specific methodologies, assumptions, and trade-offs between two computational inference methods and benchmarking frameworks (BEELINE and TENET);
3. Gain hands-on experience in applying tools and interpreting results using multiple GRN inference methods on simulated and public scRNA-seq datasets;
4. Discuss current bottlenecks, gaps in the field, and opportunities for future work.

Intended audience and level:
Beginner or intermediate level. This tutorial is aimed at bioinformaticians or computational biologists with some experience in scRNA-seq data analysis (or NGS methods) and basic statistics knowledge. We expect participants to be beginners but with minimal experience analysing next-generation sequencing datasets. The workshop will be conducted in Python/ JupyterLab and prior experience with Python programming and using command-line tools is needed. Participants will be provided with pre-processed count matrices (both simulated and real-datasets). All the analysis (JupyterLab notebooks) and steps undertaken in the tutorial will be provided via GitHub.

Maximum Participants: 30

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Room: F
Sunday, July 10, 11:00 am – 6:00 pm CDT

Organizer(s):
Luca Pinello, Harvard Medical School/Broad Institute, United States
Basheer Becerra, Bioinformatics & Integrative Genomics Ph.D. Candidate, Harvard Medical School
Maya Talukdar, Health Sciences & Technology M.D./Ph.D. Student, Harvard Medical School/Massachusetts Institute of Technology, United States
Jayoung Ryu, Bioinformatics & Integrative Genomes Ph.D. Candidate, Harvard Medical School, United States
Lucas Ferreira, Postdoctoral Fellow, MGH/Boston Children’s Hospital/Harvard Medical School, United States

The easy programmability of CRISPR-associated nucleases and other recent editors such as base and prime editors has revolutionized our ability to interrogate genome function and pinpoint causal variants. In particular, CRISPR genome engineering tools can be deployed to uncover functional important genes, pathways, non-coding elements, and examine the effects of regulatory variants on gene expression and other phenotypes.

In this tutorial, we will cover the computational workflow involved in performing CRISPR screens through both lectures of theoretical concepts and hands-on workshops of computational tools. We will begin with introducing CRISPR genome editing and common CRISPR screening strategies. Next, we will discuss computational methods to design CRISPR perturbations by generating guide RNA protospacer sequences. We will then cover experimental and computational methods to quantify genome editing activity. Lastly, we will cover computational methods to analyze and interpret the results of CRISPR screens. Ultimately, this tutorial will provide a comprehensive and holistic overview in the design and analysis of CRISPR screens without requiring any prior background in genome editing.

Learning Objectives:

• Understanding of common CRISPR editing technologies and how they are used in forward-genetics screens to interrogate genes, variants, and other regions potentially associated with a phenotype-of-interest.
• Understanding the experimental workflow of arrayed and pooled CRISPR screens with a focus on cell viability and cell sorting.
• Strategies and practical considerations when defining screen targets and generating a CRISPR guide library design (such as off-target prediction, PAM constraints, predicted cleavage site, etc.).
• Ability to use computational tools for generating CRISPR guide sequences for library design such as CRISPOR and CRISPRme.
• Ability to use computational tools for quantifying genome editing activity such as Synthego ICE and CRISPResso.
• Understand strategies in screen design for maximizing statistical power to detect a signal-of-interest.
• Ability to use computational methods for the analysis of common CRISPR-based bulk or single-cell screens with MAGeCK and SCEPTRE.

Intended audience and level:
Our target audience are researchers with an interest in analyzing CRISPR screens with little to no prior knowledge in CRISPR/Cas9 or genome editing screens or corresponding computational tools. We do require some knowledge in using command line tools and programming languages for the workshops, specifically the basics of using Python and R. We recommend knowledge in biology and statistics at an undergraduate level to fully understand the concepts discussed in the lectures.

Maximum Participants: 40

Relevant Files

• Slides

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Organizer(s):

Ana V Conesa, Spanish National Research Council, Spain
Toby Hunt, European Bioinformatics Institute, GENCODE
Anoushka Joglekar, Weill Cornell Medicine (Tilgner Lab)
Matthias Leinhard, Max Planck Institute for Molecular Genetics (Herwig Lab)
Haoran Li, The Ohio State University (Au Lab)
Alessandra Martinez, Institute for Integrative Systems Biology, Paterna, Valencia (Conesa Lab)
Dennis Mulligan, University of California at Santa Cruz (Brooks Lab)
Fairlie Reese, University of California at Irvine (Mortazavi Lab)
Andre Sim, Genome Institute of Singapore (Gorke lab)

Long read, single molecule sequencing platforms such as Nanopore and Pacbio are increasingly being used for transcriptomics analysis leading to the long reads RNA-seq (lrRNA-seq) datasets. Over the last years, these two sequencing platforms have improved in throughput and accuracy, and novel algorithms have been developed to analyze the data. Still, there are not yet clear guidelines on how the best method for accurate lrRNA-seq analysis is and how different methods compare to each other. The LRGASP is a community-wide initiative to benchmark long reads sequencing platforms, library preparation method and analysis pipelines using lrRNA-seq (https://www.gencodegenes.org/pages/LRGASP/). More than 50 different datasets were created and analyzed by a dozen of lrRNA-seq analysis tools. Evaluation metrics were created to assess the accuracy of predicted transcript models and quantification of gene and transcript expression. In this tutorial we will present the LRGASP analysis framework, discuss relevant results and lessons learned from the LRGASP project and train participants in the utilization of a diversity of pipelines for the analysis of both Nanopore and Pacbio lrRNA-seq data, as well as the LRGASP evaluation tools to assess the quality of the data. The aim of the tutorial is to provide an intensive training in tools for lrRNA-seq analysis and discuss best practiced for the analysis of these data. We will also discuss how LRGASP evaluation tools can be used to benchmark new or updated lrRNA-seq analysis tools developed by the community beyond the LRGASP contest.

The tutorial will introduce the LRGASP contest, datasets and benchmarking tools, including the OpenEBench implementation of LRGASP. Hand-ons will be provided by developers of different lrRNA-seq analysis tools on how to use their methods both for transcript identification, quality control, quantification, visualization and differential expression analysis. These include FLAIR (Brooks Lab), TALON (Mortazavi Lab), SWAN (Mortazavi Lab), IsoTools (Herwig lab), IsoQuant (Tilgner Lab), Bambu (Goke lab) , SQANTI (Conesa lab) and tappAS (Conesa lab).

This tutorial will include a wide variety of tools for both Nanopore and Pacbio RNA-seq tools, as well as an extensive benchmarking framework for this type of applications.This tutorial will contribute to disseminating good analysis practice among the transcriptome community starting to use long reads sequencing in their analysis.

Intended audience and level:
Beginner or intermediate. This tutorial will be of broad interest to researchers from academia or industry who started to analyze Nanopore and Pacbio long reads transcriptomics dataset and need guidance on alternative analysis methods. The tutorial is also useful for developers of lrRNA-seq analysis tools as it presents an extensive benchmarking platform and gives access to the utilization to competing tools by their developers.
Attendees are expected to have basic Unix command line skills and some familiarity with R/Rstudio. Programming knowledge is not required though most of the tools are written in Python.

Software/hardware requirements:
Attendees are expected to supply their own laptops and have installed R/RStudio and the tools included in the tutorial. We will be using a shared instance in AWS for those programs that require heavy computation. Instructions on how to install all software tools will be provided to participants ahead of the tutorial and a zoom session will be organized before the meeting to troubleshoot any installation problems

Maximum Participants: 40

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Room: G
Sunday, July 10, 11:00 am – 6:00 pm CDT

Organizer(s):
Yasasvini (Yash) Puligundla, Broad Institute, United States
Ian Fore, National Cancer Institute, United States

The Global Alliance for Genomics and Health (GA4GH) is an international technical standards-setting organization, enabling genomic data sharing. Through its standards, GA4GH aims to promote a federated model of data sharing, in which researchers can seamlessly access data from multiple sources in an international network using common tools and protocols, and data providers can securely share data with trusted researchers while still maintaining ownership and control over their data. In this tutorial, we explore four GA4GH standardized API interfaces that enable federated data access and analysis. The first API standard, Data Repository Service (DRS), provides minimal metadata and access information about files that can be used as input to analytical workflows. The second standard, Workflow Execution Service (WES), enables researchers to remotely run workflows defined in Common Workflow Language (CWL), Workflow Description Language (WDL) or Nextflow on an input dataset of interest. The third standard, Data Connect, allows researchers to search and filter biomedical datasets based on criteria of interest. Lastly, GA4GH Passports grants researchers fine-grained permission sets for data and compute resources they are allowed to access, and is used to control researcher access to resources behind the other three APIs.

In the first section of the tutorial, we use GA4GH-aware client tools to reach out to real-world data platforms that have adopted the four API standards, including systems maintained by NIH, Seven Bridges, ELIXIR, and DNAstack. On these platforms, we search and obtain access to controlled datasets, ultimately using them as inputs to an analysis workflow of interest.

In the second section of the tutorial, we deploy a server implementation network of the four API standards using a reference implementation suite known as the GA4GH Starter Kit. Using the same set of client tools, we run the same search, access, and analyze protocol on our local GA4GH network.

Overall, tutorial participants will gain with hands-on experience with the core GA4GH standards that enable federated analysis, from both the perspective of the researcher making use of these web services, and the data provider setting up secure, GA4GH-compliant services.

Learning Objectives for Tutorial:

• Gain an understanding of the key GA4GH standards in controlled data access, data discovery, and workflow execution, and how they enable federated genomic analysis
• Learn about and establish accounts with some of the major data platforms implementing GA4GH standards
• Run simulated federated analyses on these platforms via standardized patterns and protocols outlined in GA4GH specifications.
• Set up a local network of GA4GH web services using out-of-the-box implementations, the GA4GH Starter Kit.

Intended audience and level:
Intermediate to Advanced

• Attendees should be familiar with a programming language (code/script examples will mainly be done in Python), and have some understanding of web programming principles, such as REST APIs. Students should ideally have knowledge of containerization technologies such as Docker, as this will be used to set up the Starter Kit.
• full breakdown of the technologies that should be set up on attendees’ laptops will be distribvute prior to the tutorial.
• Attendees to have any prior knowledge of GA4GH or GA4GH Standards.
• If participants wish to access controlled access data in dbGaP to which they have access they should ensure their accounts are in good standing and have the requisite user credentials. Note that participants must know and abide by the terms of the Data Use Agreements or other terms under which they have been granted access to data.

Maximum Participants: 40

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Room: I
Sunday, July 10, 11:00 am – 6:00 pm CDT

Organizer(s):
Claudia Solis-Lemus, University of Wisconsin-Madison, United States
Douglas Bates, University of Wisconsin-Madison, United States
Sam Ozminkowski, University of Wisconsin-Madison, United States
Bella Wu, University of Wisconsin-Madison, United States

Julia has been called the programming language of the 21st century for scientific computing, data science, and machine learning. As a high-level, high-performance, dynamic language, Julia is faster than other scripting languages because of smart design decisions like type-stability through specialization via multiple-dispatch. Julia's code can be efficient and concise, which leads to clear performance gains. In addition, Julia's environments are fully reproducible and it is easy to express object-oriented and functional programming patterns.

This tutorial will provide an introduction to key Data Science tools in Julia such as reproducible project management with DrWatson.jl, data management with Arrow.jl and Tables.jl and (Generalized) linear mixed models with MixedModels.jl. Unlike widely used R packages, all packages that we will describe are written 100% in Julia thus illustrating the language’s potential to overcome the two-language problem.

This tutorial will appeal to anyone interested in learning more about Julia and some of the existing Julia packages that are already available for Statistics and Data Science. In addition to lectures, participants will engage in hands-on exercises. For example, participants will bring a dataset of their choice along with an existing script written in another language (R or python) that performs certain data analyses. During the tutorial, participants will translate their work to Julia in-order to compare running times and ease of programming.

Learning Objectives for Tutorial
At the end of the tutorial, participants will be able to:

1. Identify the main features that make Julia an attractive language for Data Science
2. Set up a Julia environment to run their data analysis
3. Organize reproducible projects with the project management of DrWatson.jl
4. Efficiently handle datasets (even across different languages) through Tables.jl and Arrow.jl
5. Fit (generalized) linear mixed models with MixedModels.jl
6. Communicate across languages (Julia, R, python)

Intended audience and level:
The tutorial is intended for any data scientist with experience in R and/or python who is interested in learning the attractive features of Julia for Data Science. No knowledge of Julia is required.

Maximum participants: 30

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Room: J
Sunday, July 10, 11:00 am – 6:00 pm CDT

Organizer(s):
Farzaneh Khajouei, Broad Institute of MIT and Harvard, United States
Elizabeth Kiernan, Broad Institute of MIT and Harvard, United States
Anton Kovalsky, Broad Institute of MIT and Harvard, United States
Tiffany Miller, Broad Institute of MIT and Harvard, United States

Biomedical data is rapidly expanding, accelerating breakthrough discoveries that can improve human health. But this poses challenges with respect to data, accessibility, cost and security. To overcome these challenges, researchers are turning to cloud computing, where a new research landscape contains interoperable, community-driven components that enable robust analyses for a variety of research needs. To harness these resources, researchers must not only understand how cloud products and platforms work but at the same time learn how they work together. In this tutorial, we will guide you through a research journey that highlights the capabilities of cloud components like Terra, Dockstore, Galaxy, and Single-Cell Portal that allow you to find data that meets your research interests, process and interrogate that data with community-developed tools, and share your reproducible analysis results. Via hands-on exercises, you will integrate tools from these interoperable platforms to complete an example end-to-end analysis with single-cell RNA sequencing data.

Learning Objectives
After the workshop, trainees will be able to:

1. Understand how Terra, Dockstore, and Galaxy interact within the cloud ecosystem.
2. Find, organize, and manipulate cloud data in Terra.
3. Find, configure, and run WDL workflows that meet data processing needs.
4. Visualize and share workflow outputs using Galaxy and Single-Cell Portal tools.
5. Apply cloud concepts by analyzing and visualizing an example single-cell RNA-seq dataset.

Intended audience and level:
Researchers and tool developers interested in ways to maximize data and analysis resources in the cloud. Coding experience is helpful, but not required, and participants should have basic familiarity with genomics terminology and standard high-throughput sequencing data formats.

Maximum Participants: 40

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Virtual Presentation - Presented through the ISMB conference platform
Wednesday, July 6, 9:00 am - 1:00 pm CDT (part 1)
Thursday, July 7, 9:00 am - 1:00 pm CDT (part 2)

Organizer(s):
Pedro de Carvalho Braga Ilídio Silva, University of São Paulo, Brazil
Renato Augusto Corrêa dos Santos,University of São Paulo, Brazil
Hemanoel Passarelli Araujo, Federal University of Minas Gerais, Brazil
Vinícius Henrique Franceschini dos Santos, University of São Paulo, Brazil

Programming skills are increasingly necessary for scientists working with biological data analysis and bioinformatics. Python has been widely used in biology and it is a high-level programming language, which makes it relatively easy to learn compared to others. In this tutorial, we introduce the first steps in analyzing biological data using Python in digital notebooks, which facilitates code documentation, real-time visualization of results, and sharing. The practice will be carried out on Google Meet and Google Colab.
Basic programming tasks will be presented, including variable assignment employing the main data structures (e.g., strings, lists and dictionaries), data types (e.g., numbers and sequences of characters), and operations (e.g., loops, comparisons, and decision structures). To provide a real example of the Python application in bioinformatics, we will use SARS-CoV-2 amino acid alignment data in a case study to apply data structures and methods from the Biopython toolkit to obtain information about different COVID-19 variants.

Learning Objectives for Tutorial:

• Introduce Google Colab digital notebooks;
• Present the basic logic and data structures in Python;
• Provide hands-on experience in analyzing biological sequences using Biopython.

Intended audience and level:
Researchers at different education levels with interest in learning programming skills for bioinformatics; level of programming skills: beginners.

Maximum Participants: 30

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Virtual Presentation - Presented through the ISMB conference platform
Wednesday, July 6, 9:00 am - 1:00 pm CDT

Organizer(s):

Sehi L'Yi, Harvard Medical School, United States
Trevor Manz, PhD Student, Harvard Medical School, United States
Qianwen Wang, Postdoctoral Research Fellow, Harvard Medical School, United States
Nils Gehlenborg Associate Professor, Harvard Medical School, United States

Most existing genomic visualization tools are tailored toward specific use cases, lacking the generalizability for reuse and expressivity to build interactive visualizations that scale to the diverse data types and analysis tasks in genomics. The Gosling visualization grammar for genome-mapped data (http://gosling-lang.org, https://pubmed.ncbi.nlm.nih.gov/34596551) defines primitives that specify how genomics datasets can be transformed and mapped to visual properties, providing building-blocks to compose unique scalable and interactive genomics data
visualizations on the web.

The Gos Python library (https://gosling-lang.github.io/gos/) is designed to enable
computational biologists to quickly author Gosling-based visualizations with their own data. In our tutorial, we introduce core concepts of genomic data visualizations and illustrate how they can be applied through hands-on training with Gos in Jupyter Notebooks.

Objectives:

• To introduce concepts of genomic data visualization
• To introduce Gosling grammar for defining interactive genomic data visualizations
• To provide hands-on experience with Gos to author interactive Gosling visualizations in Jupyter Notebooks
• To highlight how unique Gosling primitives like “semantic zooming” can be leveraged to reveal patterns across scales

Maximum Participants: 45

Relevant Files

• Setup Instructions
• Slides

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Virtual Presentation - Presented through the ISMB conference platform
Wednesday, July 6, 9:00 am - 1:00 pm CDT

Organizers:
Julian Matschinske, University of Hamburg, Germany
Julian Späth, University of Hamburg, Germany
Niklas Probul, University of Hamburg, Germany
Mohammad Bakhtiari, University of Hamburg, Germany

The vast amount of biomedical data produced by recent sequencing technologies have
shown to be a valuable resource for machine learning models to better understand biological mechanisms and pathways. While machine learning models generally depend on centralized datasets, unfortunately, this is not suited for sensitive medical data, which is often distributed across different institutions and cannot be easily shared due to high privacy or security concerns.

Federated learning, a method proposed by Google in 2017, allows the training of machine learning models on geographically or legally divided datasets without sharing sensitive data. When combined with additional privacy-enhancing techniques, such as differential privacy or secure multi-party computation, it can serve as a privacy-aware alternative to central data collections while still enabling the training of machine learning models on the whole dataset.

This is achieved by exchanging (possibly obfuscated) model parameters only. However, in such federated settings, both algorithms as well as the required infrastructure are much more complex than for centralized machine learning approaches. To address this, various federated learning tools have been developed and published recently that try to fill this gap and make the usage and development of federated algorithms easier, more intuitive, and applicable for data scientists without requiring profound software engineering capabilities.

In this tutorial, first, the theory of federated learning will be introduced using Python examples. The risk of privacy leaks is demonstrated to show the necessity of additional privacy-enhancing techniques, which are introduced afterward. The acquired knowledge will then be put to use with the help of two tools, namely PySyft¹ and FeatureCloud². These tools allow for implementing and executing federated algorithms in a truly federated production setting and will be used to provide the attendants with a practical hands-on experience, involving a real-world biomedical dataset and prediction task.
In the end, this tutorial will provide the attendants with both theoretical and practical knowledge about federated learning and privacy-enhancing techniques in the context of biomedicine and demonstrate the whole development process from the conception of the algorithm to deployment to a production system.
¹ https://github.com/OpenMined/PySyft
² https://featurecloud.ai

Learning objectives

• Federated learning theory and hands-on experience
• Privacy-enhancing techniques (differential privacy, secure-multiparty computation)
• Tools to implement federated algorithms/methods (sklearn, FeatureCloud, PySyft)
• Deployment of federated algorithms/methods

After attending the tutorial, attendants should have a solid understanding of what federated learning is, how it can be used to perform privacy-aware machine learning on distributed datasets using the techniques mentioned above, and how to practically bring such implementations to the user.

Intended audience and level:
Programming skills (ideally Python) and past experience with machine learning are advised.

Maximum Participants: 30

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Virtual Presentation - Presented through the ISMB conference platform
Thursday, July 7, 9:00 am - 1:00 pm CDT

Organizers:
Michelle M. Li, Harvard University, United States
Marinka Zitnik, Harvard University, United States

Learn more here: https://zitniklab.hms.harvard.edu/biomedgraphml/ 

Biomedical networks are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. With the remarkable success of representation learning in providing powerful predictions and insights, we have witnessed a rapid expansion of representation learning techniques into modeling, analyzing, and learning with such networks. Concretely, given a biomedical network, a representation learning method can transform the graph to extract patterns and produce compact vector representations that could be optimized for downstream tasks. Areas of profound impact include identifying variants underlying complex traits, disentangling behaviors of single cells and their effects on health, fusing electronic health records with biomedical knowledgebases to diagnose patients, and developing safe and effective treatment regimens.

In our tutorial, we will cover key advancements in graph representation learning over the last few years, with an emphasis on new opportunities in biomedicine enabled by such advancements. We will start with a technical exposition of prevailing graph learning paradigms, from classic network propagation methods to state-of-the-art graph neural networks. We will then demonstrate the impact of such techniques on accelerating research in computational biology and precision medicine. In doing so, we will present a toolbox of modern graph representation learning algorithms for biomedicine.

Intended audience and level:
The target audiences are graduate students, researchers, scientists, and practitioners in both academia and industry who are interested in applications of graph machine learning in biomedicine (Broad Interest). The tutorial is aimed towards entry-level participants with knowledge of the fundamentals of network biology and machine learning, and ideally some basic experiences in graph representation learning (Beginner or Intermediate). Although the first half of the tutorial will focus on introducing networks and predominant graph machine learning paradigms, it will be helpful to have a preliminary understanding of basic graph representation learning methods.

Materials availability. The tutorial slides and materials for hands-on exercises (e.g., code implementation, datasets) will be posted online prior to the tutorial and made available to all participants.

Maximum Participants: 100

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Virtual Presentation - Presented through the ISMB conference platform
Thursday, July 7, 9:00 am – 1:00 pm CDT

Organizer(s):
Fergus Boyles, University of Oxford, United Kingdom
Lewis Chinery, University of Oxford, United Kingdom
Tobias Olsen, University of Oxford, United Kingdom
Matthew Raybould, University of Oxford, United Kingdom

High-throughput computational methods for B-cell receptor/antibody analysis are enabling the study of deep-sequencing samples of the human repertoire. Whether applied to improve our understanding of the adaptive immune system, perform immunodiagnosis, assess vaccine performance, or generate lead molecules for therapeutic discovery, these approaches are set to become a key component of the 21st century immunologist’s toolkit.

Such in silico analysis algorithms must strike a careful balance between accuracy and
throughput, to cope with the complexity of immune repertoire samples. They tend to take the form of clustering algorithms that convert antibody repertoire sequences into clonal lineages or more general groups of molecules likely to have sufficient chemical similarity to engage the same antigens. Classically these algorithms have assessed antibody sequence properties, but structure prediction tools are now reaching the required throughput and accuracy to yield meaningful three-dimensional representations of repertoires of antibodies.

These methods promise to offer unprecedented resolution and understanding of the
sampled binding sites (‘paratopes’). We will explore these technologies through a mock in silico drug discovery case study, starting from convalescent patient repertoires that represent a trove of potential human-expressible therapeutic antibodies. You will gain hands-on experience with the latest approaches (both sequence-based and structure-based) that have the speed required to enable computational early-stage discovery directly from these repertoire sequences. We’ll first identify the convergent (seen across multiple individuals) disease-responding antibodies, analyse them for likelihood of pathogen complementarity, and finally assess them for developability concerns such as stability and humanness.

Learning Objectives:

• Use the latest techniques to cluster patient B-cell receptor repertoire sequencing data and identify convergence in pathogen response across individuals
• Use sequence-based approaches to identify convergent antibodies with a high probability of binding to/neutralising pathogens of interest
• Build 3D structural models of antibody sequences of interest and use them to develop a structural hypothesis for their mode of action
• Use a sequence-based machine learning approach to confirm that the antibody sequences are indeed fully ‘human’ (and so are unlikely to cause immunogenicity as a therapeutic)
• Use a recent structure-based method to compare candidate antibodies to late-stage clinical trial therapeutics, identifying any with extraneous biophysical properties associated with poor developability (solubility, viscosity, expression, etc.)

Intended audience and level:
This tutorial is intended for those with some prior knowledge of immunology/biology who would like to learn about functional profiling of antibody repertoires, and for those with interests in how to computationally analyse antibody repertoire datasets to discover novel therapeutics. No prior experience with sequence analysis or structural modelling tools is assumed, but familiarity with working on unix-based systems is strongly recommended for the practicals. For part of the tutorial we will use the Oxford Protein Informatics Group's suite of antibody modelling tools, which are available both as an online web server and as a Singularity container.
Prior experience of working with Singularity containers is not required, but attendees will need a working installation of Singularity if they wish to run the tools which depend on SAbDab-SAbPred on their machine.

Maximum participants: 50

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Virtual Presentation - Presented through the ISMB conference platform
Thursday, July 7, 9:00 am - 1:00 pm CDT

Organizer(s):
Afaf Saaidi, Georgia Institute of Technology, United States; Hybrid Intelligence - Capgemini Engineering, France

This tutorial will cover the available tools and web servers to visualize the structure of RNA with an emphasis on the secondary structure. While biological function could be understood through the structure, a suitable visualization appears to be a milestone to allow better identification of functional areas and better comparison between structures. Sketching the structure of RNA remains difficult from an algorithmic point of view especially when the structure contains pseudo-knots. Today we have a wide range of tools that aim to optimize the representation of the structure either using template or template-free approaches. In this tutorial, we will cover the most used tools and current web servers offering structure visualization utilities through a lecture, a demonstration of existing tools and web servers, and hands-on training sessions. The audience will be equipped with the essential knowledge to select the most appropriate tool to use when needed.

Learning objectives:

• Recall the available tools for RNA structure visualization.
• Equip the audience with the essential to know about the visualization of RNA
  structure.

Learning goals:

• To Understand the utility of each tool and become aware of the appropriate tool to use in need.
• To Become familiar with the latest visualization web servers.
• To be aware of the limitations and challenges of drawing an RNA structure.

Intended audience and level:
Computational Biologists who are dealing with RNA structure, beginner or intermediate level.

Maximum Participants: 30

Relevant Files

• Slides

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COSI Organizer Information Page

• Last update: April 11, 2022
  
  
• COSI Track Benefits
• Abstract Submission Process
• Live/Virtual Platform Talks
• General FAQ
  
  
  Schedule Overview:
  https://www.iscb.org/cms_addon/conferences/ismb2022/schedule/schedule.php
  
  

 COSI Track Benefits

• COSIs receive up to five (5) complimentary registrations. Escrow funding may be used to secure additional registrations if needed. Complimentary discount codes* were issued to COSI organizers March 30, 2022.
  
  *(Please note the code does not allow a non-member to receive the complimentary ISCB membership and will not work if entered if the free membership is chosen.)
  
  
• Speaker Funding- $1000 per COSI day to support travel of invited speakers. Funding is allocated for TRAVEL support for speakers.  Speakers who will not be presenting in-person may not take advantage of funding.  COSIs may choose to use their escrow funding to give stipends, honorarium, purchase additional registrations, etc.
• Session moderators will be required for Live from Madison talks and will be monitor questions from the virtual audience in addition to the in-person audience. These registrations can be distributed to anyone at the discretion of the COSI.
• Attendee Commissions - At the end of the conference, ISCB will calculate the COSI commissions. Commissions are based on the number of registrations that identified your group as their main COSI. A registrant may select up to four COSIs if purchasing a full conference registration. A set commission rate is applied to each paid registrant and shared based on total percentage to the COSI.
  
• Unrestricted use of escrow funds to support COSI track speakers or additional events
• Full allocation of any sponsorship raised by COSI to COSI escrows. Note: COSIs are responsible for fulfilling any benefit promised to a COSI only sponsor. Sponsors wishing to participate in the exhibit hall would need to pay the conference exhibitor fees.

Abstract Submission Process

Key Dates:

• COSIs identify 2 or 3 Abstract Chairs (ACs) from within community to manage the review process. These names will be added to EasyChair as Track Chairs for each COSI.
• COSI Abstract Chairs will be responsible for identifying a review / program committee to review the abstracts for both talk and poster presentation within their COSI. ACs will add these names to COSI track within EasyChair.
• Each COSI is responsible for reviewing abstracts submitted to their area as either:
  • Poster only
  • Talk and poster (abstracts in this category if not accepted as a talk should be reviewed for a poster).
• Ideally each abstract should have a minimum of two (2) reviews and preferably three (3).
• COSI Abstracts Chairs are encouraged to quickly review the abstracts that are submitted to their COSI. If the abstract is not topical, please let Steven Leard (This email address is being protected from spambots. You need JavaScript enabled to view it.) know and he can transfer the abstract to the appropriate COSI suggested by your COSI. We recognize abstracts may cross COSI themes. In the event that an abstract could fit in multiple theme, it will be considered first to the COSI for which the author has designated submission. If not selected for oral, it may be considered for another COSI track.
• COSI Abstract Chairs responsible for notifying acceptances for talks and posters within COSI track.
  
  
  • Notifications should be sent no later than May 12.
  • Each speaker will need to sign permissions to be part of the online platform.
  • All talk (pre-recorded) presentations must be submitted to conference platform beginning June 30 and no later than July 7, 2022.
  • Poster presentations must be submitted to conference platform beginning June 30 and no later than July 7, 2022.

• Selected Abstract talks will be presented by COSI track and run in parallel at the conference.
• The length of a talks are in units of 20 minutes (should includes time for questions). Oral presentation times for abstracts are announced by the COSI track organizers.
• COSI Area Chairs responsible for reviewing Late Posters to their COSI (opens April 25, closes May 19) within individual COSIs. *Acceptance notifications sent May 26.
• COSI Area Chairs responsible for awarding their own prizes - top poster prize winner name, affiliation and poster title should be sent to This email address is being protected from spambots. You need JavaScript enabled to view it. no later than 3:00 pm on Thursday July 14 so the name can be recognized during the closing ceremonies.
  
  

• COSI Track Schedule

  • COSIs will provide their detailed track schedule by May 31, 2022 using the template provided by ISCB.
  • Track schedule will be loaded into the online platform and will be the guiding production schedule.
  • COSIs needs to indicate on the track schedule which talks will are live-stream or will have live Q&A, panels, or breakout room requirements.

  
  COSI Invited Talks

  • COSI Track Chairs will provide to ISCB their confirmed invited speakers (name, affiliation, email) no later than May 27.

  
  Posters

  • All abstracts accepted to present posters will receive instruction on how to enter their poster into the conference platform.
    • ISCB will use the abstract, title, author list, as entered in EasyChair
    • Each poster entry will have PDF of poster and recording of presentation

  
  Speaker Communication

  • ISCB will handle the communications with your speaker on how to:
    • Use the conference platform if they are presenting virtually.
    • Upload their presentation to the conference platform.
  • All presenters must be registered for the conference. You can assign complimentary passes as you wish or cover additional passes from your COSI escrow.
  • ISCB also has a fellowship program if one is unable to pay. Fellowships are prioritized based on career level and income status of the country.

  
  Day of Logistics and Track Execution

  • COSIs will be responsible for monitoring their tracks on their scheduled presentation day.
    • Recommend to assign 2-3 individuals that will share the work on monitoring the track.
    • COSI session moderators are to ensure Q&A, panel, breakout rooms stay on schedule.

Live/Virtual Platform Talks

Live from Madison

Presenters will be expected to be in-person in Madison. Those unable to travel will be presented live stream through the conference platform to those attending live in the Madison presentation room and also live through the platform for virtual participants.

Presenters will use the provided podium computer (PC) to present slides. Video of the presenter is captured with in-room webcam placed on mic stand in front of podium. Audio and slides are captured through in-house AV system.  A volunteer technical moderator (VTM) is responsible for ensuring the image, slides and sound are transmitted/available through the conference platform to virtual participants. Meeting rooms will also be serviced by a volunteer room assistant responsible to support the VTM, AV staff and virtual platform technicians.

A session moderator (COSI volunteer) will be responsible for introductions, keeping talks on-time and for moderating questions from the audience - due to time considerations likely one question from the live and one from the virtual audience will be considered.  

All presenters will be required to provide a pre-recorded talk for the virtual platform library in advance of the conference. The pre-recorded talk will be available shortly after the live presentation to provide faster and more seamless access to the conference content for virtual participants.

Volunteer technical moderators will receive training virtually (2-3 weeks prior to conference) and again on-site (Saturday, July 9) by both AV and Platform providers.

Draft Acceptance Letter:

Congratulations your submission has been accepted for a talk and/or poster at ISMB 2022 as part of the XXX COSI. Detailed talk schedules will be available early June and posted on the conference programme pages at https://www.iscb.org/ismb2022

Please take a moment to review these details:

• One author must be registered to present the talk and/or poster for the conference. Registration instructions are available at: https://www.iscb.org/ismb2022-register
• Presenters must be registered by June 13. Your registration ID is required to link your participation with talks and /or posters.
• If you are attending in-person in Madison and requiring a hotel you can find booking details at: https://www.iscb.org/ismb2022-general/hotels
• If you have been accepted for a talk and your planned participation in ISMB 2022 has changed from what you indicated during submission (presenting in Madison, or virtually) please notify the COSI organizers directly so they can schedule accordingly.
• Presenters of posters and talks will receive a confirmation of participation link that must be completed no later than June 13. This will be emailed directly to you from ISCB.
• ISCB is pleased to offer fellowships to any ISCB member in good standing with priority going to members from low or middle-income countries as well as students and postdoctoral fellows to attend ISMB 2022. Details are available here: https://www.iscb.org/ismb2022-general/travel-fellowships
• While all presentations will be presented live (from Madison, or virtually) all presenters will be required to provide a pre-recorded talk for the virtual platform library. Pre-recorded talks can be uploaded through the conference platform beginning June 30. The pre-recorded talk will be available shortly after the live presentation to provide faster and more seamless on-demand access to the conference content. Additional details on recording requirements will be available in early June.
• Poster presentation details are available at https://www.iscb.org/ismb2022-program/posters The page will continue to be updated as confirmations of poster participation is received. All poster presenters will upload a 5 - 7 minute video to the virtual conference platform site along with a PDF of their poster beginning June 30 and no later than July 7. The video is part of a video library all registered delegates will be able to view through the conference platform.
• If youhave questions about your presentation please contact the COSI organizers directly.

 General FAQ

Q: Can I submit more than one abstract?
A: Yes, but although having the same person deliver more than one talk is permitted, it is not encouraged. Although a poster presenter may present two posters (one in Poster Session A and one in Poster Session B), we encourage labs to involve multiple presenters.

Q: Can previously accepted work be considered for a poster?
A: Yes, we do ask that you note the year the work was published and provide the Digital Object Identifier (DOI) during the submission process.