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ISMB/ECCB 2021
Day 2, Highlights & Recap!

ISMB/ECCB 2021

 

Day 2: Highlights & Recap!

 

ISMB/ECCB 2021 Day 2 picked up right were Day 1 left off.  From Population scale analysis of human sequence data to Teaching the Instagram generation, it was another day filled with science and ideation.  Today's ISCBdaily is filled with track highlights and tips to enhancing your virtual conference experience.

Highlights
Opening the day was the ISCB Town Hall Meeting (slide deck posted to ISCB booth), where attendees gathered to learn about the state of ISCB which is strong even in the face of these continued unprecedented times. Christine Orengo, ISCB President, gave a brilliant address thanking those who serve, recognizing the Society achievements, and highlighting her vision over the next three years.

Congratulations to all the ISCB Competition Winners:

2021 Wikipedia Winners
Nelly Selem Mojica & Erika Cruz, improvements to the Pan-genome
Tiago Lubiana, Biocuration
Wyatt Smith & anonymous user 'Sauxeris', Out-of-bag error
Nelly Selem Mojica, David Alberto García Estrada, Guillermo Rodríguez Guerrero, María Teresa Alvarez Zúñiga, Mario Jardón Santos, Camila Silva Gomez, Fernando Mauricio Rivera Vega, Hermes Bolivar-Torres, Tania Raquel Garibay Valladolid, Jacobo Sevillano Serrano, Richar Chacon Serna, Daniel Santana Quinteros, and the anonymous users 'JFCR07' and 'Gonzalo corlop', Machine learning in bioinformatics

Welcome Newly Elected Members of the Board of Directors
Bonnie Berger, MIT
Francisco De La Vega, Tempus Labs, Inc.
Laxmi Parida, IBM Research
Lucia Peixoto, Washington State University

CONGRATULATIONS, ISCB STUDENT COUNCIL!
Amazing work is being done by this group.  From Regional Student Group formation and collaboration, to assisting with placing interns.  The energy, commitment, and passion is contagious.

Well done, SCS 2021
Being held virtually again in 2021, the Student Council Symposium did not disappoint.  Over 200 participants from around the world gathers on Thursday and Friday to enjoy excellent keynotes, share their research and network with one another.  ISCB shows deep appreciation to Cleidy Osorio, Chair, and Victor Grentzinger, co-Chair, and the entire team, congratulating them on a job well done.

At the conclusion of the Town Hall, participants enjoyed nine scientific tracks, and capping off day 2 was a robust and engaging keynote address on Cells in Space: Methods to investigate local neighborhoods of cells delivered by the ISCB Overton Prize Keynote, Barbara Engelhardt.


 
 
COSI Recaps

Hitseq
Our first Hitseq session on Sunday 25th featured new methods for the analysis of genomes and transcriptomes using long reads. The adaptive sampling during nanopore sequencing by Weilguny allows optimal usage of sequencing effort and we discovered how Bionano long reads can be used to study the coupling of promotor and enhancers methylation. The statistics of kmers was for the first time discussed, new graph-based methods to assembly and compact genomes were presented and we learnt about the structure of the centromere with Olga Kunyavskaya. Our highlight was our keynote Angela Brooks who presented her lab's effort to characterize isoform changes in cancer using Nanopore and the LRGASP challenge for evaluation of long-read RNA sequencing methods.

EvolCompGen
The first day of the Evolution and Comparative Genomics (EvolCompGen) COSI featured 8 talks. The talks illustrated the broad use of phylogenetic trees and networks, such as calibrated species tree inference, individual cell lineage reconstruction, or admixture event inference. Consistent with the zeitgeist, we also witnessed creative uses of machine learning approaches for comparative genomics analyses—to speed up orthology prediction, to detect copy number variation, and to infer co-evolving genes from phylogenetic profiling. We look forward to days 2 and 3 of EvolCompGen! Join us on Cafe Connect and our new community Slack (https://bit.ly/evolcompgen)!
 
 
Career Center and Jobs Board
Looking for that perfect candidate?  Looking for a job?  Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Cheat-Sheet Section/Platform Tips:
From time to time we may experience technical issues.  When in doubt, give the system a quick refresh!

Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability.  In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated.  Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).
*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.

 
Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recording

 
When in doubt, give the system a quick refresh!
*Live presentations such as COSI keynote talks, panels, and the Distinguished Keynotes are being processed and may take up to 48 hours to fully post.
 
 
Cast Your Ballot!
Members!!  Make your voice heard - Cast your ballot today!
 
ISCB Election - Polls are Open
 
 

Tomorrow, Tuesday, July 27: Highlights & Reminders

11:00 UTC: COSI Tracks: HitSeq, 3Dsig, CompMS, EvolCompGen, Education, RegSys, BioVis, NetBio
11:00 UTC: Special Session New developments in AI for Integrating imaging and genomic data
11:00 UTC: NIH/ODSS Special Track
14:20 UTC: ISCB Public Affairs and Policy Session: Science Communication and Science Journalism
15:20 UTC: Research Exchange Forum for Birds of a Feather (BoFs)
15:20 UTC: Poster Session C: 3Dsig, BioVis, CompMS, Education, EvolCompGen, HitSeq, NetBio, RegSys, TransMed
15:20 UTC: 
Exhibitor Demos:  Exhibitor Demos: PerMedCoE, EMBL-EBI, GOBLET,
EMBL-EBI, de.NBI
16:20 UTC ISCB Distinguished Keynote: Eduardo Rocha
17:20 UTC:
Daily Closing Comments
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 3, Highlights & Recap!

ISMB/ECCB 2021

 

Day 3: Highlights & Recap!

 

What a day ISMB/ECCB 2021 just had! Half way through the conference and still going strong. Day 3 dove straight into 10 tracks of science from 7 different COSI sessions, one special session on New developments in AI for Integrating imaging and genomic data, another on Science Communication and Science Journalis, and finally the NIH/OD Office of Data Science Strategy.

Highlights
Day 3 saw the scientific sessions give way to the Distinguished Keynote address by Eduardo Rocha on Horizontal gene transfer driven by self-mobilizable genetic elements allows the acquisition of complex adaptive traits and their transmission to subsequent generations. Transfer speeds up evolutionary processes as exemplified by the acquisition of virulence traits in emerging infectious agents and by antibiotic resistance in many human pathogens. Transfer is also costly because the vectors of horizontal transfer compete within genomes, have their own mobile elements and are often deadly. As a result, genomes are repositories of multiple immune systems from hosts and from mobile elements that interact in complex ways to drive gene flow in communities. The combination of evolutionary genomics and sequence analysis is now opening up these processes to show how they bring into the genome a constant flux of novel genes that favor the establishment and the invention of novel functions.



Special Session Recaps

EDI Panel Discussion Takes Center Stage at NIH ODSS Track (ISMB 2021)
Dr. Susan Gregurick, Director of NIH ODSS, organized and co-chaired with Dr. Karol Watson, Professor of Medicine in the Division of Cardiology at the David Geffen School of Medicine at UCLA, a vibrant panel discussion on "Diversity in Data Science Training and Research."

An array of data science experts from underrepresented groups, coming from academic institutions (e.g., Hispanic-Serving Institutions, HSIs; Historically Black Colleges & Universities, HBCUs), legal industry, and technology industry tackled critical questions focusing on issues of equality, diversity, and inclusion (EDI) in multiple dimensions of data science training and research:

How do we define, measure and operationalize EDI? EDI concepts can mean different things in different settings, and there is no “one size fits all” approach. What must we do to gain support for EDI beyond procedural compliance or symbolic initiatives? What mechanisms do we apply to increase the diversity and/or cultural competence of those involved in data science training? What are the appropriate metrics for evaluating our progress?

Public Affairs & Policy Committee - Science Communication and Science Journalism
The COVID-19 pandemic has brought science into the limelight of public perception in an unprecedented fashion. Scientists have become more present in the media, accelerated transmission of new results has been effected by the public starting to pay attention to unreviewed research reports, journalists have been faced with the requirement to bring such emerging results to the public on short notice. Today's panel moderated by Thomas Lengauer, ISCB's Immediate Past President, focused on challenges facing both scientists and members of the media. Panelists, Kai Kupferschmidt, Independent Science Journalist, Emma Hodcroft, University of Bern, John Moult, Institute for Bioscience and Biotechnology Research (IBBR), and Freya Robb, Science Media Centre, joined to discuss issues on how to best effect communication to the public on science results and also and especially on the science process.

*Live session should be posted within 24 to 48 hours. Please make sure to check back for the recordings and keep the conversations going*


COSI Recaps


BioVis
The first day of BioVis started with a keynote by Seán O’Donoghue about inter-disciplinary practices in biological visualization. Seán shared his experiences using mixed practices in approaching several scientific challenges for instance, in multi-omics and genetic variation analysis, and shared reflections on establishing visualization as a powerful technique. The keynote was followed by an invited talk delivered by Liz Marai on their RuleBender paper that received our newly introduced Test of Time Award, which is given out to an influential paper published at BioVis at least 10 years ago. The following two sessions focused on visualization in the field of genomics as well as cellular and omics data. Besides short talks for abstracts, there was one ISMB proceedings talk and an invited highlight talk given by Jen Rogers. In the evening, a virtual social event was held, which included a memorial for Michel Westenberg, who passed away earlier this year. He was a well-known and highly regarded member of the BioVis community.

The second day started with talks focusing on the integration of visualization and machine learning techniques. While some of the talks explored explainability issues within deep learning techniques for drug repurposing and analysis of high-dimensional data, others looked into how hierarchical visualization and association-focused techniques could support the analysis of transcriptome data and single cell RNA-seq datasets. The next set of talks, featuring another ISMB proceedings and an invited highlight talk by Helena Jambor, introduced new techniques to visualize imaging data using some innovative techniques such as visual exemplars, and novel glyph based representations that serve as pictorial summaries, as well as empirical research outlining best practices for producing effective images in publications. The closing session featured a keynote talk by Jessica Hullman who shared her research and insights on uncertainty visualizations, and how models of inference can transform our understanding of how people reason with data visualizations.

CompMS
The CompMS COSI wrapped up a successful two days on Tuesday. The first day focused on computational metabolomics, and started off with a keynote by Dr. Theodore Alexandrov on how computational mass spectrometry enables spatial and single-cell metabolomics. On the second day Dr. Vadim Demichev shared his views on recent advances enabling high-throughput proteomics during the opening keynote, and during the closing keynote Dr. Ed Huttlin presented the BioPlex project for biological discovery of the 'social network' within a human cell. Additionally, the program featured 15 oral presentations during which speakers discussed a wide range of computational mass spectrometry metabolomics and proteomics advances. Topics reached from developments in single-cell metabolomics, over machine-learning applications in proteomics, all the way to exciting new developments for screening interactome data.

EvolCompGen
We had another exciting day at the Evolution and Comparative Genomics (EvolCompGen) COSI featuring eight talks and several posters coming in from at least three continents. They spanned a variety of subjects from the evolution of proteins, domains, gene content, tumor cells to evolutionary events such as horizontal gene transfer, endosymbiotic gene transfer, copy number alterations, tandem duplication of protein domains and DNA repair through non-homologous-end-joining. We also got to see more examples of machine-learning applied to evolutionary analysis and an exciting webapp for characterizing protein using molecular evolution. Finally, we ended the day with more discussion of domain evolution and linguistic methods applied to cancer. While we miss in-person interactions, we have had a good time connecting with COSI members on Cafe Connect and Slack!

Join us tomorrow for the third and final day of our COSI – not just on Zoom but also on Cafe Connect, and our new community Slack (https://bit.ly/evolcompgen). Also, don’t forget to partake in our closing panel discussion at 14.40 UTC, Jul 28!

Don't Forget to Visit Our Exhibitors!

 
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Cheat-Sheet Section/Platform Tips:
From time to time we may experience technical issues. When in doubt, give the system a quick refresh!

Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).

*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.

 
Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recording

 
When in doubt, give the system a quick refresh!
*Live presentations such as COSI keynote talks, panels, and the Distinguished Keynotes are being processed and may take up to 48 hours to fully post.
 
 
Cast Your Ballot!
Members!! Make your voice heard - Cast your ballot today!
 
ISCB Election - Polls are Open
 
 

Tomorrow, Wednesday, July 28: Highlights & Reminders

11:00 UTC: COSI Tracks: MLCSB, CAMDA, Function, EvolCompGen,
RegSys, Microbiome, TextMining, iRNA
11:00 UTC: Special Session Emerging gain-of-function mutations and their characterization by multi-omics network biology
11:00 UTC: NIH/ODSS Special Track
15:20 UTC: Research Exchange Forum for Birds of a Feather (BoFs)
15:20 UTC: Poster Session D: CAMDA, Education, EvolCompGen, Function, iRNA, MICROBIOME, MLCSB, RegSys, Text Mining
15:20 UTC: Exhibitor Demos:
PerMedCoE: Core applications PhysiCell-MPI, PhysiBoSS COBREXA and CellNOpt/CARNIVAL
15:20 UTC:
Exhibitor Demos:
PerMedCoE: Core applications PhysiCell-MPI, PhysiBoSS COBREXA and CellNOpt/CARNIVAL
EMBL-EBI: New training website and upgraded online tutorials
GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training
EMBL-EBI: Curated course collections and new training materials collections
de.NBI: Introduction to de.NBI / ELIXIR-DE and the de.NBI cloud
16:20 UTC ISCB Distinguished Keynote: Kate Jones
17:20 UTC:
Daily Closing Comments
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 4, Highlights & Recap!

ISMB/ECCB 2021

 

Day 4: Highlights & Recap!

 

ISMB/ECCB 2021 keeps the science going into day 4 with 10 tracks of innumerable opportunities for discovery, as well as networking and connections for all attendees. Day 4 highlighted 8 different COSI sessions, one special session on Emerging gain-of-function mutations and their characterization by multi-omics network biology, and day 2 of the NIH/OD Office of Data Science Strategy.

Highlights
Distinguished Keynote, Kate Jones gave an enlightening talk on Our Planet, Our Health - Ecosystem approaches to forecasting zoonotic diseases. Today we live longer and more prosperous lives than ever before, as a species we have made huge advances to create conditions for better health for billions of people, however this progress is taking a heavy toll on the planet's natural systems. Kate explored the links and interdependencies between our health and the health of our planet with particular reference to understanding how rapid global environmental change impacts the emergence and spread of high impact infectious diseases like Ebola or Covid. She also discussed how recent advances in the resolution and coverage of remote-sensing satellite data and cutting-edge machine-learning algorithms open up the possibilities of developing global early warning systems to prevent and manage future epidemics.


 

*Live sessions will be posted within 24 to 48 hours for rendering & editing. Please make sure to check back for the recordings and to keep the conversations going*


COSI Recaps

CAMDA
Virtual CAMDA 2021 took off to a full house, with the well over 100 delegates likely grateful that they didn't have to cram into a real room, while reducing their carbon footprint by 50 tons of carbon dioxide. Opening the session, Professor Francesca Ciccarelli of the Francis Crick Institute highlighted advances in predicting cancer driver genes not just at the cohort level but for individual patients, and their cumulative effects in age. This was followed by a variety of contributions by CAMDA delegates from Cambridge, Isarel, Kyiv, and Stanford, who exploited an impressive variety of modern AI language models to identifying scientific papers relevant to drug induced liver injury, as benchmarked by a CAMDA challenge organized jointly with the US FDA with support of IARAI Vienna. The session was rounded off by reports on testing the robustness and reproducibility of computational genomics tools, an in silico evaluation of SARS-CoV-2 primer performance, and an intriguing study of mechanistic models of COVID-19 infection and antiviral interventions. Join us on Thursday for keynotes by Director Weida Tong (NCTR/FDA) about AI myths and their implications on regulatory science, and Director Nikos Kyrpides (DOE Joint Genome Inst) cover Microbiome Data Science from the Earth Microbiome to the Global Virome. The Thursday sessions will then cover studies of antimicrobial resistance and its relationship to phages, as well as a new set of reports on using AI to identify papers on adversarial drug reactions - join us for the talks and lively discussion on the round tables! Programme details also at www.camda.info

EvolCompGen
On the last day of our EvolCompGen COSI, we featured seven enriching presentations on a variety of topics concerning the evolution of genomes, genes, or at the intermediate level of “syntenies” (chromosomal gene clusters). At the gene level, we discussed quantification of introgression (gene flow between species), convergent evolution, phylogenetic profiling, and the identification of new metabolic pathways. At the genome level, we had talks on whole-genome duplication, and more specifically an innovative method for allo-polyploidy versus auto-polyploidy prediction was highlighted. A new model to infer tumor phylogeny and call variants using single-cell data was also presented. The closing talk was on Super-Reconciliation, a novel method for inferring the evolution of syntenies through segmental duplications and HGTs. This presentation made the bridge with the panel discussion, where we discussed a variety of open questions on ancestral genome reconstruction, orthology prediction, and unifying methods for synteny evolution.

The capstone of this year's Evolution and Comparative Genomics track was a panel discussion focusing on the evolution of chromosomal gene clusters, ancestral genome reconstruction, and phylogenetic comparative methods. A spirited discussion ensued touching on tradeoffs between computational costs and accuracy and how the rapid growth of genomic data sets influences this tradeoff, the pros and cons of parsimony versus probabilistic models, hybrid approaches that attempt to assess uncertainty while preserving the speed of parsimony and how such methods can be used to infer convergent evolution, and, finally, whether convergent evolution introduces noise in phylogenetic inference. These discussions aroused so much interest and generated such a lively exchange amidst the panelists, moderators, and participants, that we continued brainstorming for another full hour in a new Zoom e-space after the session ended officially. We wrapped up our three-day COSI enriched with new ideas and new collaboration perspectives.

Stay tuned for award/poster winners and special mentions during the ISMB/ECCB 2021 closing session!

iRNA
The iRNA COSI 2021 kick-off was given by Manuel Irimia who provided a fascinating keynote on the evolution of alternative splicing networks and the extent of their tissue conservation. Today’s contributed talks focused on mRNA stability, circular RNA evolution and prediction, the study of transcriptomics in health-related applications and tools for the analysis of 3D RNA structures. Our first day ended with entertaining flash talks / quiz and poster session.

Text Mining
TM COSI featured two outstanding keynotes, one by Dr. Pysalo (University of Turku) highlighting the evolution of transformers in the biomedical field and opportunities for collaboration. The second keynote was a joint presentation by Dr. Ball (FDA) and Dr. Hirschman (MITRE), reporting on the quest for text mining methods to modernize post-market drug safety assessment at FDA, the needs and challenges, followed by a description of results from the evaluation of methods for automated extraction of adverse drug events, and experiments with humans-in-the-loop. The session selected talks covered applications of text mining methods (both traditional machine learning and Deep learning) across various fields, including -omics (metagenomics, annotations of -omics samples), protein folding, clinical discharge letters, biocuration, and science communication. The COSI ended with the text mining spotlight section with two talks. First, Dr. Lu described efforts at NCBI to bring to the community freely available tools and methods that have been developed in light of their own needs, with a focus on LitSuggest, a web-based system for biomedical literature recommendation and curation, and on TeamTat an annotation tool for team collaboration. Finally, Dr. Poon from Microsoft Health Futures provided an overview of PubMedBERT, and its advantages over other BERT-based models in the biomedical domain.

RegSys
Spread over three days, and attracting approximately 100 attendees in each session, RegSys presented cutting-edge research in regulatory & systems genomics. We enjoyed exciting keynote talks from Céline Vallot, Fabian Theis, Anaïs Baudot, Olga Troyanskaya, Camille Berthelot, and Juanma Vacquerizas, along with four proceedings papers and seventeen contributed talks.

Day 1 focused on advances in characterizing cell type-specific regulatory networks using single cell assays. The keynotes, in particular, demonstrated the power of applying single cell technologies to characterize epigenomic features of cancer drug resistance, and regulatory relationships in large-scale perturbation screens. Day 1 closed with several interesting talks that featured different ways to characterize cooperative interactions between transcription factors.

Day 2 broadened the track themes. Inspirational keynotes integrated multi-modal data types using increasingly powerful computational techniques, yielding insights into the mechanisms underlying human diseases. Day 2 contributed talks spanned themes such as profiling cell-specific splicing events, determining the impact of viral integration events, and analyzing nucleosome features on cell-free DNA.

Day 3 turned to the theme of comparative regulatory genomics, with a keynote and contributed talk characterizing how cell-specific enhancers have evolved across mammals. Day 3 also focused on advances in profiling the three-dimensional organization of the genome. Talks demonstrated methods for increasing the resolution of chromatin interactions, while a keynote cast doubt on whether genome organization influences gene expression.

A steady theme throughout all days and sessions was the growing adoption of neural network techniques in regulatory genomics, with interesting methodological advances demonstrated in several application domains. We had a very enjoyable virtual program overall, and we encourage the RegSys community to continue our conversations on the RegSys slack channels:
https://join.slack.com/t/regsyscommunity/shared_invite/zt-tprp1q5g-pNcDNiFUXyJQacdfY1nGWg

Exhibitor Spotlight:



EMBL-EBI Demo Presentations:

Track Content:

Introduction to EMBL-EBI resources
A guide to EBI search

 
Start your morning off right and head over to the Expo Showcase for the Exhibitor Demos. Grab some coffee and get ready to learn and discover.
 

Don't Forget to Visit Our Exhibitors!

 
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Cheat-Sheet Section/Platform Tips:
From time to time we may experience technical issues. When in doubt, give the system a quick refresh!

Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).

*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.

 
Miss a talk? Watch it On-Demand!
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recordings
• The virtual platform and content will be available to attendees following the conference until November 30, 2021.
 

*Live sessions will be posted within 24 to 48 hours for rendering & editing. Please make sure to check back for the recordings and to keep the conversations going*

 
 
Cast Your Ballot!
Members!! Make your voice heard - Cast your ballot today!
 
ISCB Election - Polls are Open
 
 

Tomorrow, Thursday, July 29: Highlights & Reminders

10:30 UTC: Exhibitor Demos:
EMBL-EBI: Using the EMBL-EBI Competency Hub to support you career development
PerMedCoE: Competency Hub and upcoming training
GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training
11:00 UTC: COSI Tracks: MLCSB, CAMDA, Function, VarI, BOSC, SysMod, Microbiome, iRNA
11:00 UTC: General Computational Biology Track
12:40 UTC: Final Project Presentations: Collaborative Tools for Protein Analysis Hackathon 2021
15:00 UTC: Tech Track: Accelerating Multi-stage Bioinformatic Pipelines with Big Memory, Jingchao Sun, MemVerge
15:20 UTC: Research Exchange Forum for Birds of a Feather (BoFs)
15:20 UTC: Poster Session E: BIOINFO-CORE, BOSC, CAMDA, COVID-19,  EvolCompGen, Function, iRNA, MICROBIOME, MLCSB, RegSys, Special Session 05, SysMod, Text Mining, VarI, General Comp Bio
16:20 UTC ISCB Innovator Award Keynote: Ben Raphael
17:20 UTC:
Daily Closing Comments
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 6 - Conference Highlights & Things to Know

ISMB/ECCB 2021

 

Friday, July 30: Highlights & Reminders

HAPPY LAST DAY! Don't forget to pop over to the Research Exchange Forum and pay a visit to our amazing Exhibitors!
 
11:00 UTC: COSI Tracks: MLCSB, CAMDA, BioInfo Core, VarI, BOSC, SysMod, iRNA
11:00 UTC: Covid-19 Special Track & Panel: This panel will compare different models to access, share and protect COVID-19 data, evaluate their advantages, limitations and complementarity to prevent and control pandemics.
11:00 UTC: Special Session: Single Cell and Spatial Data Analysis
11:00 UTC: Technology Track:

11:00-11:20
Phyre2 and Missense3D: Protein structure prediction and missense variant analysis
11:20-11:40
Using CATH-Gene3D v4.3 and its resources to predict the structure and function of novel protein sequences
11:40-12:00
DeepChain: A platform for protein design
12:00-12:20
Developing a reusable and versatile virtual bioinformatics training platform in the de.NBI cloud
12:40-13:00
The EMBL-EBI search and sequence analysis tools APIs and their role during the current COVID-19 pandemic
13:00-13:20
The European COVID-19 Data Portal – Accelerating COVID-19 Research through Open Data Sharing
13:20-14:00
PerMedCoE: A roadmap to scalability in Personalized Medicine
14:20-14:40
The GenePattern Notebook Environment
14:40-15:20
Integrated Pathway/Genome/Omics Informatics in Pathway Tools and BioCyc GenePattern Notebook Environment

   
15:20 UTC: ISCB Accomplishments by a Senior Scientist Award Keynote: Peer Bork

16:20 UTC: Awards and Closing Ceremony
 

Exhibitor Spotlight:



PerMedCoE Demo Presentations:

Track Content:
A Roadmap to Scalability in Personalised Medicine, by José Carbonell
HPC-enabled multiscale simulation to uncover mechanistic insights in the COVID-19 infection
PerMedCoE Building Blocks, by Henrik Nortamo
PerMedCoE Building Blocks & Workflows design, by Javier Conejero
PhysiCell-MPI / PhysiCell-X, by Gaurav Saxena
Multiscale modeling with PhysiBoSS, by Vincent Noël
COBREXA.jl: Metabolic Modeling on HPC, by Miroslav Kratochvil
CellNOpt / CARNIVAL, by Bartosz Bartmanski
The PerMedCoE Competency Framework, by Marta Lloret-Llinares
PerMedCoE Training Activities, by Daniel Thomas López

EMBL-EBI Demo Presentations:
Track Content:
Bioinformatics training: Curated course collections and new training materials
New EMBL-EBI training website and upgraded online tutorials

 
 

Don't Forget to Visit Our Exhibitors!

 
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Cheat-Sheet Section/Platform Tips:
From time to time we may experience technical issues. When in doubt, give the system a quick refresh!

Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).

*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.

 

Miss a talk? Watch it On-Demand!
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recordings
• The virtual platform and content will be available to attendees following the conference until November 30, 2021.

 
Anyone else sneaking in some Olympics viewing between the #ISMB/ECCB21 sessions? Share your best scientific session/Olympic viewing set up from this week and don't forget to tag the Conference!
 
 
Cast Your Ballot!
Members!! Make your voice heard - Cast your ballot today!
 
ISCB Election - Polls are Open
 
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 5 - Conference Highlights & Things to Know!

ISMB/ECCB 2021

 

Thursday, July 29: Highlights & Reminders

10:30 UTC: Exhibitor Demos:
EMBL-EBI: Using the EMBL-EBI Competency Hub to support you career development
PerMedCoE: Competency Hub and upcoming training
GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training
11:00 UTC: COSI Tracks: MLCSB, CAMDA, Function, VarI, BOSC, SysMod, Microbiome, iRNA
11:00 UTC: General Computational Biology Track
12:40 UTC: Final Project Presentations: Collaborative Tools for Protein Analysis Hackathon 2021
15:00 UTC: Tech Track: Accelerating Multi-stage Bioinformatic Pipelines with Big Memory, Jingchao Sun, MemVerge
15:20 UTC: Research Exchange Forum for Birds of a Feather (BoFs)
15:20 UTC: Poster Session E: BIOINFO-CORE, BOSC, CAMDA, COVID-19, EvolCompGen, Function, iRNA, MICROBIOME, MLCSB, RegSys, Special Session 05, SysMod, Text Mining, VarI, General Comp Bio
16:20 UTC ISCB Innovator Award Keynote: Ben Raphael
17:20 UTC:
Daily Closing Comments
 
Start your morning off right and head over to the Expo Showcase for the Exhibitor Demos at 10:30 UTC.  Grab some coffee and get ready to learn & discover.
 

Don't Forget to Visit Our Exhibitors!

 
ISCB Election - Polls are Open
 
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Platform Tips:


Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).

*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.


Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recordings
• The virtual platform and content will be available to attendees following the conference until November 30, 2021.


When in doubt, give the system a quick refresh!

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 4 - Conference Highlights & Things to Know!

ISMB/ECCB 2021

 
Wednesday, July 28: Highlights & Reminders
 
11:00 UTC: COSI Tracks: MLCSB, CAMDA, Function, EvolCompGen,
RegSys, Microbiome, TextMining, iRNA
11:00 UTC: Special Session Emerging gain-of-function mutations and their characterization by multi-omics network biology
11:00 UTC: NIH/ODSS Special Track
15:20 UTC: Research Exchange Forum for Birds of a Feather (BoFs)
15:20 UTC: Poster Session D: CAMDA, Education, EvolCompGen, Function, iRNA, MICROBIOME, MLCSB, RegSys, Text Mining
15:20 UTC: Exhibitor Demos:
PerMedCoE: Core applications PhysiCell-MPI, PhysiBoSS COBREXA and CellNOpt/CARNIVAL
15:20 UTC:
Exhibitor Demos:
PerMedCoE: Core applications PhysiCell-MPI, PhysiBoSS COBREXA and CellNOpt/CARNIVAL
EMBL-EBI: New training website and upgraded online tutorials
GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training
EMBL-EBI: Curated course collections and new training materials collections
de.NBI: Introduction to de.NBI / ELIXIR-DE and the de.NBI cloud
16:20 UTC ISCB Distinguished Keynote: Kate Jones
 

Don't Forget to Visit Our Exhibitors!

 
ISCB Election - Polls are Open
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 
 

Platform Tips:


Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).

*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.


Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recording


When in doubt, give the system a quick refresh!

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 2 - Conference Highlights & Things to Know

ISMB/ECCB 2021

 

Tuesday, July 27: Highlights & Reminders

11:00 UTC: COSI Tracks: HitSeq, 3Dsig, CompMS, EvolCompGen, Education, RegSys, BioVis, NetBio
11:00 UTC: Special Session New developments in AI for Integrating imaging and genomic data
11:00 UTC: NIH/ODSS Special Track
14:20 UTC: ISCB Public Affairs and Policy Session: Science Communication and Science Journalism
15:20 UTC: Research Exchange Forum for Birds of a Feather (BoFs)
15:20 UTC: Poster Session C: 3Dsig, BioVis, CompMS, Education, EvolCompGen, HitSeq, NetBio, RegSys, TransMed
15:20 UTC:
Exhibitor Demos: Exhibitor Demos: PerMedCoE, EMBL-EBI, GOBLET,
EMBL-EBI, de.NBI
16:20 UTC ISCB Distinguished Keynote: Eduardo Rocha
17:20 UTC:
Daily Closing Comments
 
ISCB Election - Polls are Open
 
Career Center and Jobs Board
Looking for that perfect candidate? Looking for a job? Look no further than the Conference Jobs Board located at:
https://www.iscb.org/cms_addon/conferences/ismbeccb2021/jobpost/jobs/jobs.php
 

Platform Tips

 

Updating the Time zone
The ISMB/ECCB 2021 virtual platform is enabled with time zone localization to enhance usability. In order to set the platform to your local time zone, click on "Full schedule" and then click on the dark grey "My Time Zone" box to ensure it is activated. Once clicked, the box will darken in color and your schedule will automatically be viewed in your local time zone.

Struggling with UTC conversion - UK +1 CEST +2 EDT -4, CDT -5, MDT -6, PDT -7, AEST +10, Tokyo +9, Beijing +8

Roundtables
Don't forget you can video-chat & network with up to 15 people at the Café Connect “Roundtables” (https://ismbeccb2021.showcare.io/roundtables/).
*Roundtables are pre set up for each COSI (including BOSC), and you can also create your own roundtable!
 
Navigating the Platform
The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.
 
Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recording

 
When in doubt, give the system a quick refresh!
 
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Day 2 - Conference Highlights & Things to Know

ISMB/ECCB 2021

 
ISCB Election - Polls are Open
 

Monday, July 26: Highlights & Reminders

10:00 UTC: ISCB Town Hall Meeting (LIVE)
11:00 UTC: COSI Tracks: HitSeq, 3Dsig, CompMS, EvolCompGen,
Education, RegSys, BioVis, TransMed, Bio-Ont, NetBio
15:20 UTC: Research Exchange Forum includes Posters and Exhibitors / BoFs
15:20 UTC:
Exhibitor Demos: PerMedCoE, EMBL-EBI, GOBLET, EMBL-EBI, de.NBI
16:20 UTC ISCB Overton Prize Keynote: Barbara Engelhardt
17:20 UTC:
Daily Closing Comments
 

Platform Tips

To access the virtual conference platform, you must log-in from the email sent to you with the subject line: Welcome to ISMB/ECCB 2021 – July 25-30. This email arrived directly from the conference platform provider Showcare (This email address is being protected from spambots. You need JavaScript enabled to view it.) and will have instructions on how to log-in. Please ensure you check your Junk/Spam folder. If you cannot find this email, please email This email address is being protected from spambots. You need JavaScript enabled to view it..

Navigating the Platform

The ISMB/ECCB 2021 virtual platform is divided up into several areas:

• Sessions
• Full Schedule
• Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
• Café Connect
• Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.


Miss a talk?
• Go to Full Schedule in the left-hand menu
• Use the back arrow to see a previous day’s sessions
• Select a session and the session box will pop up
• Click on the title you wish to view
• This will take you to the on-demand recording


When in doubt, give the system a quick refresh!
 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

 
 

ISMB/ECCB 2021
Welcome!

ISMB/ECCB 2021

 
ISCB Election - Polls are Open
 

Welcome to ISMB/ECCB 2021!

 

Let your curiosity take over, discover the latest research in the field and get ready to connect, collaborate, and engage! Registration is still open if you would like to join us for six science and networking filled days - https://www.iscb.org/ismbeccb2021-registration.

To access the virtual conference platform, you must log-in from the email sent to you with the subject line: Welcome to ISMB/ECCB 2021 – July 25-30. This email arrived directly from the conference platform provider Showcare (This email address is being protected from spambots. You need JavaScript enabled to view it.) and will have instructions on how to log-in. Please ensure you check your Junk/Spam folder. If you cannot find this email, please email This email address is being protected from spambots. You need JavaScript enabled to view it.

Navigating the Platform

The ISMB/ECCB 2021 virtual platform is divided up into several areas:

  • Sessions
  • Full Schedule
  • Research Exchange Forum which includes Exhibitors, Posters and Birds of a Feather sessions.
  • Café Connect
  • Your Personal Profile

You can always return to the main page by using Home Lobby button in the upper left or at the top of your screen. The left menu can be collapsed or expanded simply by clicking on the 3 bars on the top left corner. We recommend you take advantage of the in-platform tutorial at the bottom left called ‘Get Started’. This will walk you through not only your profile updates but other aspects of the platform as well.

Sunday, July 25: Highlights & Reminders

11:00 UTC: COSI Tracks: HitSeq3DsigTransMedBio-Ont
11:00 UTC: Special Session: Computational Biology going Green
11:00 UTC: Special Session: Representation learning in biology
11:00 UTC: WEB2021: Making training materials FAIR - experiences, challenges, solutions
15:20 UTC: 
Research Exchange Forum includes Posters and Exhibitors / BoFs
16:20 UTC ISMB/ECCB Distinguished Keynote: Rodrigo A. Gutierrez
17:20 UTC:
Daily Closing Comments
 

Thank you to our generous sponsors!



Harvard Medical School Department of Biomedical Informatics

 
 

 International Society for Computational Biology (ISCB)
 

ISCB Leadership Election: Polls are Open!

 

ISCB members have the privilege to nominate and elect members of the ISCB community to hold leadership positions. The 2021 open officer positions are Vice President and Treasurer. The 2021 ballot also contains the leadership election of the ISCB Student Council. 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 leadership positions. You are encouraged to take a moment to cast your vote.

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.