ISMB 2020

Day 3, July 15, 2020 Highlights & Recap

DAY 3: Highlights & Recap

Day three of the conference kicked into high gear with Conference Co-chair, Shoshana Wodak awarding the ISCB Overton Award to the third keynote of the conference, Jian Peng, PhD, University of Illinois at Urbana-Champaign. His engaging presentation focused on Machine learning for structural and functional genomics resulting in a lively Q&A period.

The day then dove right back into the many sessions, tracks and channel options.

Lunch & Learn
The Black Women in Computational Biology Network held today's Lunch and Learn where conference attendees learned about its founding, mission and were able to participate in a lively discussion.

Two New NIH ODSS Awards
RFA-OD-20-013 - RADx-UP Coordination and Data Collection Center (CDCC) (U24 Clinical Trial Optional)

description as per the FOA: "NIH is issuing this FOA in response to the declared public health emergency issued by the Secretary, HHS, for 2019 Novel Coronavirus (COVID-19). This emergency cooperative agreement funding opportunity announcement (FOA) from the National Institutes of Health (NIH) provides an expedited funding mechanism as part of the Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) initiative, a consortium of community-engaged research projects to understand factors that have led to disproportionate burden of the pandemic on the underserved and/or vulnerable populations so that interventions can be implemented to decrease these disparities. This FOA seeks to fund a single Coordination and Data Collection Center (CDCC) as an integral part of the consortium."
Letters of intent were due July 8 but as per Dr. Brennan some flexibility in NIH due dates will be acceptable due to COVID-19.
See also corrections in NOT-OD-20-140, including changes to total amounts awarded: "NIH intends to commit up to $80 Million over four years to fund one award."

The Artificial Intelligence for BiomedicaL Excellence (AIBLE) program - more details here.

This program will produce "Rubrics that allow evaluation of datasets (and plans to generate datasets) for ML-readiness, Tools to accelerate the creation of ML-ready data sets (intelligent annotators, metadata-filling instruments), Infrastructure to host, disseminate, and promote tools and datasets, and a group of ethically sourced, clean and available AI-ready datasets."
This is a broad initiative planned to last 7 years.

Virtual Art Exhibit
Find the Beauty in Science and pursue the amazing submissions to the 2020 Art in Science Competition, including the top three winners announced at the ISCB Town Hall.

Virtual Poster Hall
Be sure to peruse the Virtual Poster Hall. All posters were pre-recorded along with a PDF of the poster to view. If you have questions about specific posters, review the schedule for when presenters will be available for live Q&A here.

Bioinformatics Bazaar
Don't forget to visit the Bioinformatics Bazaar, the conference attendee grab bag of crowd-sourced products, services, and tools.

Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the ISMB 2020 Jobs Board.

OnDemand Talks - How to access
Below is a quick how to video to help you access all the on-demand content.

How to access OnDemand content

Patience is a virtue
We ask for your patience as we work to process the previous days content and place it into the system for on-demand access. It is no easy task to process more than 300 talks and we are working as quickly as possible to get this done. REMEMBER: you will have access to this platform and all of the scientific content until the end of October. Thank you in advance for your understanding and PATIENCE.

Green ISCB: ISCB Groves
ISCB, in partnership with All Things Small and Green and Trees for Life, has set up its first grove of native trees, the ISCB 2020 grove, to offset carbon emissions caused by ISCB activities such as those emitted during the conferences, workshop or panel meetings that it organizes. With this grove, ISCB members are also offered a simple and convenient way to offset their own carbon emissions such as those incurred during traveling to ISCB conferences or workshops. We welcome you to join us as we work towards healing our environment.

ISCB Equity, Diversity & Inclusion Survey
To update your member profile and complete the ISCB EDI survey, please follow the following steps:

Click on the My ISCB tab once you have signed into the ISCB website
Click on "edit" then immediately "update your profile" button above your profile image
Choose the Membership Record tab from the Edit Your Details section
Scroll down and update the ethnicity section making sure to click the blue Update section when finished.

Cheat-Sheet Section

To access any session of your choice, please go to "Watch Now" and select the Channel for that specific Track. When in doubt, always refresh (F5)!

Cast Your Ballot - Polls close Thursday, July 16!

See you all tomorrow for the final day of ISMB 2020!

ISMB 2020

Wednesday, July 15

Today @ ISMB 2020

Let your curiosity take over, discover the latest research in the field and get ready to connect, collaborate, and engage!

Highlights & Reminders

07:45 AM	Posters available for viewing

09:30 AM	ISCB Overton Prize Award Keynote: Jian Peng

10:40 AM	COSI Track Presentations: 3DSIG, Bio-Ontologies, HiTSeq, RegSys, BioVis, CompMS, Microbiome, NetBio, TransMed, VarI

01:15 PM	Lunch & Learn: The Black Women in Computational Biology Network

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Cafe Connect
Connect with your COSI for networking opportunities. Click on your COSI image to access networking rooms. If you want to just grab a room with a friend, go to Cafe Connect Open Table.

ioinformatics Bazaar
Don't forget to visit the Bioinformatics Bazaar, the conference attendee grab bag of crowd-sourced products, services, and tools.

Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the ISMB 2020 Jobs Board.

OnDemand Talks - How to access
Below is a quick how to video to help you access all the on-demand content.

How to access OnDemand content

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Thank you to our sponsors!

Silver Sponsors

Harvard Medical School - The Department of Biomedical Informatics (DBMI) in the Blavatnik Institute

Copper Sponsors

Great Lakes Bioinformatics (GLBIO) conference

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Conference Exhibitors

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Montréal food

We know you are missing the regional cuisine of the Quebec province of Canada and Montreal. Join us in celebrating Montreal cuisine by showing us your own dish inspired by favorite dishes that will change daily.

Post your photos on social media using these hashtags #ISMB2020 and #ISMB2020virtualeats and tag @iscb and @meetmontreal for today's Poutine challenge!

https://www.mtl.org/en/experience/la-poutine-week

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Exploring Montréal from Home

It’s sad that we cannot be gathered together in Montreal to experience the city, our science, and see our friends and colleagues. To help ease the pain, Tourisme Montréal has compiled a list of some of the best online activities, including virtual city tours, music, games and more which feature the city. ISMB will be going back to Montreal in 2024 but until then, enjoy these activities.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

ISMB 2020

Day 2, July 14, 2020 Highlights & Recap

Day 2: Highlights & Recap

What a day! Thomas Lengauer kicked off the day after the morning welcome with the presentation of the ISCB Outstanding Contributions Award to Judith Blake, PhD, Professor, The Jackson Laboratory. Congratulations!

Highlights

The conference continued right into the science with the awarding of the ISCB innovator Award to the second keynote of the conference's Xiaole Shirley Liu, PhD, Professor, Biostatistics, Harvard T.H. Chan School of Public Health. Her dynamic presentation focused on Computational modeling of tumor immunity.

The day then dove right back into the many sessions, tracks and channel options.

NIH/ODSS Special Track
The NIH/OD Office of Data Science Strategy (ODSS) held a full day of cutting edge research presentations and plenty of intense and interactive discussions.

Lunch & Learn
F1000Research held the first Lunch and Learn of the conference focusing on Innovative Open Access publishing for software tools and beyond. The talk give an introduction to the F1000Research publishing platform, how the open publishing model works and how we’ve collaborated with various Bioinformatics communities to ensure the platform is somewhere easy and effective to publish articles on software.

Virtual Poster Hall
Be sure to peruse the Virtual Poster Hall. All posters were pre-recorded along with a PDF of the poster to view. If you have questions about specific posters, review the schedule for when presenters will be available for live Q&A here.

Bioinformatics Bazaar
Don't forget to visit the Bioinformatics Bazaar, the conference attendee grab bag of crowd-sourced products, services, and tools.

Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the ISMB 2020 Jobs Board.

OnDemand Talks - How to access
Below is a quick how to video to help you access all the on-demand content.

How to access OnDemand content

Cheat-Sheet Section

To access any session of your choice, please go to "Watch Now" and select the Channel for that specific Track. When in doubt, always refresh (F5)!

Cast Your Ballot!

See you all tomorrow for another exciting and engaging day!

ISMB 2020

Tuesday, July 14

Today @ ISMB 2020

Let your curiosity take over, discover the latest research in the field and get ready to connect, collaborate, and engage!

Accessing Talks
To access any session of your choice, please go to "Watch Now" and select the Channel for that specific Track.

Cafe Connect
Connect with your COSI for networking opportunities. Click on your COSI image to access networking rooms. If you want to just grab a room with a friend, go to Cafe Connect Open Table.

Highlights & Reminders

07:45 AM	Posters available for viewing

09:30 AM	ISMB Distinguished Keynote: Xiaole Shirley Liu

10:40 AM	COSI Track Presentations: CAMDA, Function / CAFA, iRNA, MLCSB, Education, EvolCompGen, SysMod

10:40 AM	Special Track: NIH/OD Office of Data Science Strategy

10:40 AM	Special Sessions SST03: Bioinformatics of Corals

01:15 PM	Lunch & Learn: F1000 Research – Innovative Open Access publishing for software tools & beyond

02:00 PM	Special Sessions SST04: SCANGEN: Single-cell cancer genomics SST05: HuBMAP: Integrating genomics, imaging and mass-spectrometry to construct single-cell human tissue maps

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Thank you to our sponsors!

Silver Sponsors

Copper Sponsors

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Conference Exhibitors

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Montréal food

Post your photos on social media using these hashtags #ISMB2020 and #ISMB2020virtualeats and tag @iscb and @meetmontreal for each day’s challenge!

https://www.mtl.org/en/experience/sugaring-around-montreal

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Exploring Montréal from Home

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

ISMB 2020

Day 1, July 13, 2020 Highlights & Recap

Day 1: Highlights & Recap

We are off to a good start! A huge thank you to everyone for joining ISMB 2020 from all over the world. Today was a full day of innovation, stellar science and amazing opportunities.

Tech Improvement

And of course, a stellar day could not be complete without a few hiccups so thank you for hanging in there with us as we worked through the technical issued that occurred. THANK YOU FOR YOUR UNDERSTANDING AND PATIENCE! Below please take note of our "cheat sheet section" with some helpful hints to navigate the smaller technical problems that arose today and hopefully provide a smoother tomorrow.

Highlights

ISMB 2020 opened with a bang. The conference opening keynote was Elaine Mardis who gave an engaging and enthusiastic keynote address on Computational Analysis in Pediatric Cancer Precision Medicine.

The day then dove right into the new and exciting world of a virtual conference with a vast array of sessions, tracks and channels.

ISCB Town Hall

ISMB marked the largest attended ISCB Town Hall in its history with over 250 attendees joining to hear about the state of ISCB which is strong even in the face of these unprecedented times.

Congratulations to all the ISCB Award & Competition Winners:

ISCB Student Software Award Winner
Florian Schmidt
TEPIC

ISCB Student Software Prospective Future Impact Award Winner
Robert Ietswaart
GeneWalk

ISCB Art in Science
Dr. Zdenko Herceg, Art of Epigenetics
Mr. Joshua Bugbee, Impact
Dr. Marwan Abdellah, Brain Vasculature

2020 Wikipedia Winners
Diego Mariano, Structural Bioinformatics
Tiago Lubiana, OBO Foucndry & List of OBO Foundry Ontologies
Darko Durovski, Transcriptomics

Green ISCB: ISCB Groves

ISCB, in partnership with All Things Small and Green and Trees for Life, has set up its first grove of native trees, the ISCB 2020 grove, to offset carbon emissions caused by ISCB activities such as those emitted during the conferences, workshop or panel meetings that it organizes. With this grove, ISCB members are also offered a simple and convenient way to offset their own carbon emissions such as those incurred during traveling to ISCB conferences or workshops. We welcome you to join us as we work towards healing our environment.

Equity, Diversity & Inclusion Strategic Plan Announced

ISCB Equity, Diversity & Inclusion Committee develops ISCB first strategic plan related equity, diversity and Inclusion. The elements of the plan are:

1. Increasing social accountability for change in the Society
2. Obtaining data and developing measures to assess progress
3. Voluntary training: The “ISCB Awareness toolkit”
4. Recruitment initiative
5. Mentoring

More information will be posted to a special section of the ISCB website soon.

ISCB Equity, Diversity & Inclusion Survey

To update your member profile and complete the ISCB EDI survey, please follow the following steps:

1. Click on the My ISCB tab once you have signed into the ISCB website
2. Click on "edit" then immediately "update your profile" button above your profile image
3. Choose the Membership Record tab from the Edit Your Details section
4. Scroll down and update the ethnicity section making sure to click the blue Update section when finished.

Cheat-Sheet Section

To access any session of your choice, please go to "Watch Now" and select the Channel for that specific Track. When in doubt, always refresh (F5)!

Miss a session? Not to worry!
Session will be available for on demand viewing as well.

Cast Your Ballot!

See you all tomorrow for another exciting, engaging and technically smooth day!

Welcome to ISMB 2020!

Let your curiosity take over, discover the latest research in the field and get ready to connect, collaborate, and engage!

Log in to the conference platform and build your attendee profile at:
https://iscb-ismb20.myconferencenow.com/login/ and navigate ISMB 2020 like a pro!

Monday, July 13: Highlights & Reminders

07:45 AM	Posters available for viewing

09:30 AM	ISMB Distinguished Keynote: Elaine Mardis

10:40 AM	COSI Track Presentations: CAMDA, Function / CAFA, iRNA, MLCSB, SysMod, Text Mining, BioInfo Core

10:40 AM	Technology Track Presentations: The GenePattern Notebook Environment Expression Atlas: A platform for integrating and displaying expression data from tissues to single cells HiSCiAp: User-friendly, scalable tools and workflows for single-cell analysis

10:40 AM	Special Sessions SST01: Systems Immunology: Computational approaches for understanding human immune system and immune-related diseases

01:00 PM	ISCB Town Hall

02:00 PM	WEB 2020

02:00 PM	Special Sessions SST02: Bioinformatics outside the lab: How to mobilize online citizen scientists to accelerate research SST01 continues

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Thank you to our sponsors!

Silver Sponsors

Copper Sponsors

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Montréal food

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Exploring Montréal from Home

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

ISMB 2020
HURRY! Register Online Today

Acquire new knowledge, new tools, new contacts... Register today and experience the endless possibilities of virtual ISMB 2020!

Choose from ISCB COSI Tracks, posters, and keynotes representing a multidisciplinary forum for the dissemination of the latest developments in computational biology/bioinformatics.
-Explore the Program-

Online Registration Deadline: TODAY July 9, 2020
Conference will be conducted in the Eastern Daylight Time Zone
(convert schedule to your time zone here)

Register To Attend

Book Your Tutorial Spot!
Tutorial Registration Deadline: TODAY July 9, 2020 9 AM Eastern

ISMB 2020 Register for Online Workshop and Tutorial Program

Tutorial Registration

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Mark your calendars for TOMORROW, the 7th of July!

Please use the link below to find more information or to register for:

July 07, 2020 at 11:00AM EDT, Genetic Basis Of De Novo Appearance Of Carotenoid Ornamentation In Bare-Parts Of Canaries by Malgorzata Gazda, hosted by EvolCompGen COSI and SMBE.

Unlike wild and domestic canaries (Serinus canaria), or any of the three dozen species of finches in genus Serinus, the domestic urucum breed of canaries exhibits bright red bills and legs. This novel trait offers a unique opportunity to understand the mechanisms of bare-part coloration in birds. To identify the mutation producing the colorful phenotype, we resequenced the genome of urucum canaries and performed a range of analyses to search for genotype-to-phenotype associations across the genome. We identified a nonsynonymous mutation in the gene BCO2 (beta-carotene oxygenase 2, also known as BCDO2), an enzyme involved in the cleavage and breakdown of full-length carotenoids into short apocarotenoids. Protein structural models and in vitro functional assays indicate that the urucum mutation abrogates the carotenoid-cleavage activity of BCO2. Consistent with the predicted loss of carotenoid-cleavage activity, urucum canaries tended to have increased levels of full-length carotenoid pigments in bill tissue and reduced levels of carotenoid-cleavage products (apocarotenoids) in retinal tissue compared with other breeds of canaries. We hypothesize that carotenoid-based bare-part coloration might be readily gained, modified, or lost through simple switches in the enzymatic activity or regulation of BCO2 and this gene may be an important mediator in the evolution of bare-part coloration among bird species.

Register for an ISCB Webinar

International Society for Computational Biology

Polls are Open!

ISCB members have the privilege to nominate and elect members of the ISCB community to hold leadership positions. The 2020 open officer positions are Vice President and Secretary. The polls are now open for you to cast your vote for members who have accepted nominations for these leadership positions. It is your voice as a member of this prestigious organization to elect these officer positions. You are encouraged to take a moment to cast your vote.

Vice President


*Alex Bateman, Ph.D.*	*Nicola Mulder, Ph.D.*	*Russell Schwartz, Ph.D.*

Secretary


*Michelle Brazas, Ph.D.*	*Lucia Peixoto, Ph.D.*

Cast your ballot for these important leadership positions

*ISCB members in good standing receive one vote for each open position. To access the ballot, log into My ISCB and click on the link provided in this email or the ISCB Election link in the left-hand menu.

Mark your calendars for TOMORROW, the 30th of June!

Please use the link below to find more information or to register for:

June 30, 2020 at 11:00AM EDT, Global surveillance of COVID-19 by mining news media using a multi-source dynamic embedded topic model by David Buckeridge, an ISCB COVID-19 Webinar

As the COVID-19 pandemic continues to unfold, understanding the global impact of non-pharmacological interventions (NPI) is important for formulating effective intervention strategies, particularly as many countries prepare for future waves. We used a machine learning approach to distill latent topics related to NPI from large-scale international news media. We hypothesize that these topics are informative about the timing and nature of implemented NPI, dependent on the source of the information (e.g., local news versus official government announcements) and the target countries. Given a set of latent topics associated with NPI (e.g., self-quarantine, social distancing, online education, etc), we assume that countries and media sources have different prior distributions over these topics, which are sampled to generate the news articles. To model the source-specific topic priors, we developed a semi-supervised, multi-source, dynamic, embedded topic model. Our model is able to simultaneously infer latent topics and learn a linear classifier to predict NPI labels using the topic mixtures as input for each news article. To learn these models, we developed an efficient end-to-end amortized variational inference algorithm. We applied our models to news data collected and labelled by the World Health Organization (WHO) and the Global Public Health Intelligence Network (GPHIN). Through comprehensive experiments, we observed superior topic quality and intervention prediction accuracy, compared to the baseline embedded topic models, which ignore information on media source and intervention labels. The inferred latent topics reveal distinct policies and media framing in different countries and media sources, and also characterize reaction COVID-19 and NPI in a semantically meaningful manner.

Register for an ISCB Webinar

ISCB News and Announcements

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Polls are Open!

More Articles ...

ISCB On the Web