Leading Professional Society for Computational Biology and Bioinformatics
Connecting, Training, Empowering, Worldwide

ISCB News and Announcements

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY) In-Person

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY)

In-Person
December 2 - 4, 2021
Viceroy Hotel - Snowmass/Aspen, Colorado
Registration Open

The eighteenth conference is a meeting of the International Society for Computational Biology (ISCB) held each year in Snowmass, Colorado. The Rocky series began nineteen years ago as a regional conference, and has grown into an international program with a spotlight on regional development in the computational biosciences. The presenters of the Rocky conference are early and late career research scientists representing a broad spectrum of universities, industrial enterprises, government laboratories, and medical libraries from around the world.

The conference is a chance to get to know your colleagues near and far, seek collaborative opportunities, and find synergies that can drive our field forward.

The conference includes short "flash" presentations (10 minute talks), poster presentations and keynote presentations on current projects including significant works-in-progress involving the application of advanced computational methods to significant problems in biology or medicine.

The Rocky conference is also a great opportunity for early career researchers to be selected to present their work.  

Check out discounts for groups from one project or institution.  

Visit the website for more information: www.iscb.org/rocky2021

2021 ISCB Rocky Mountain Bioinformatics Conference (ROCKY) In-person
 

 ISCBacademy Webinar: COSI Series
 
Register today for the next ISCBacademy Webinar!
 
Please use the link below to find more information or to register for:
 

September 7, 2021 at 11:00 AM EDT - ISCBacademy COSI Series: 3D SIG by Mohammed AlQuraishi, Columbia University - Hosted by 3D SIG

AlphaFold2 burst on the life sciences stage in late 2020 with the remarkable claim that protein structure prediction has been solved. In this talk I will argue that in some fundamental sense the core scientific problem of static structure prediction is finished, but that further maturation is necessary before AlphaFold2 and similar systems can address biological questions beyond those of structure determination itself. I will outline some of these necessary developments and highlight one in particular: the prediction of structure from individual protein sequences. I will describe present challenges and opportunities, and our efforts to tackle them by combining advances in protein language modeling with end-to-end differentiable structure prediction, presenting new results on the prediction of orphan and de novo designed proteins. Time permitting, I will end by speculating on what abundant availability of structural information might mean for the future of biology.

Hosted by:

3D SIG - The International Society for Computational Biology

 
 
Register for an upcoming ISCB Webinar
 

 
International Society for Computational Biology
 

ISCB Announces Results of the
2021 Leadership Elections


 
The Board of Directors of the International Society for Computational Biology (ISCB) is pleased to announce the results of the recent leadership elections.

Members of the society elected the following as Officers beginning January 2022:
 
Officers
Nicola Mulder, Vice President
Janet Kelso, Treasurer
 
Student Council Executive Team
R. Gonzalo Parra, Representative to the ISCB Board of Directors
Handan Melike Dönertaş, Chair
Gabriel Olguin-Orellana,Vice Chair
Ana Castillo Orozco, Secretary 
Yesid Astroz, Treasurer
 

For additional information on ISCB's annual leadership nominations and elections procedures, please see https://www.iscb.org/leadership-nominations-and-elections.

The next call for nominations of directors and officers will open February 2022, for terms beginning January 2023.
 
 
 

 

 

ISMB/ECCB 2021
Day 6, Highlights & Recap!

ISMB/ECCB 2021

 

Day 6: Highlights & Recap!

 

Well that is a wrap! The final day took off and ended with a bang. Today saw a full day of technology with the long awaited Technology Track, the final 7 COSI sessions, and the last Special Session on Single Cell and Spatial Data Analysis.

Highlights
ISCB Accomplishments by a Senior Scientist Award Keynote, Peer Bork gave a the final talk of the conference on Analyzing microbes in us and on our planet. Environmental sequencing, that is metagenomics, has become a major driver for uncovering microbial biodiversity and increasingly also for cataloging molecular functions on our planet. The exponentially increasing metagenomes need computational tools and resources to allow researchers to access and digest these valuable data. Based on methods and resources, developed in their group, but also utilizing public bioinformatics resources, here he introduced into their work on the gut microbiome, aimed at basic understanding, but also at medical applications, showing a few examples from tracing the structure and function of microbiomes in different habitats on earth (ocean and soil) and briefly outlining the concept of interacting computational resources, developed and maintained by a network of researchers across Europe.


 

COSI Recaps

Bioinfo-Core
The Bioinfo-Core COSI session brought together managers and staff working in bioinformatics core facilities around the world. The excellent work done in the following core facilities was presented:

  • Nicole Scherer from the Brazilian National Cancer Institute talked about the hard work and challenges of establishing a core facility from the ground up in a hospital.
  • Gregg TeHennepe from The Jackson Laboratories talked about applying the methods of tools of Agile project management to bioinformatics research support, and presented a case study of a real-life case.
  • Fatima Mitterboeck from Agriculture and Agri-Food Canada presented on the Bioinformatics Research Support Network, community of practice sharing best practices and working towards supporting users at a national scale.
  • Fleur Gahwens presented about building up a bioinformatics community at the Dutch Institute of Ecology, and shared the lessons learned during the development of the epiGBS2 Snakemake-based workflow in that community.
  • Krishna Karuturi from The Jackson Laboratories discussed the comprehensive approach for embracing machine learning and imaging advances in that organization, and the linkages and collaborations required to make that a reality.
  • Ning Zhang from the Stowers Institute presented RiboSeeker, an end-to-end package that integrates a Snakemake workflow and an R package for ribosome profiling.


Our keynote speaker Johannes Köster presented on Snakemake, one of the most widely used and cited workflow management systems. Snakemake's new approaches for modularization and deployment and other new approaches and features were introduced to an audience of nearly 80 attendees.

After the keynote, we had our breakout room discussions where the following topics were discussed:

  1. Workflow managers / pipeline tools
  2. Training
  3. Spatial transcriptomics
  4. Project management
  5. Core facilities during the pandemic and knowledge sharing
  6. Protected data

BOSC
The second and last day of BOSC 2021 started off with a keynote talk by Thomas Hervé Mboa Nkoudou on “Contribution of the maker movement to biotechnology in Africa: An open science perspective”. This is the first BOSC keynote talk that was not given in English: Thomas spoke in his native French, with English subtitles. Thomas emphasized that open source / open data are key to wide dissemination of knowledge in the biosciences and beyond. An example of this openness in practice is the way the Maker movement, which embraces openness, has contributed to the democratization of biotechnology in Africa. Thomas observed that universities have not yet embraced openness and the maker-movement philosophy in African countries; an attendee noted that this is also the case in Europe. Thomas responded that to address this, we need to teach principles, philosophy and give practical experience as early as possible so that new generations consider maker/DIYbio solutions when they are faced with problems themselves.

In the ‘Analysis tools’ session, we heard from David Twesigomwe about a pipeline that incorporates graph based variant calling for Cytochrome genes. Patrick Kunzmann talked about updates to the Python library Biotite that performs sequence and structural analyses. Charlotte Herzeel talked about elPrep, a set of tools that has improved computing performance of popular NGS pipelines. This session also had two talks from the Broad, the first one by Bhanu Gandham on how the GATK pipeline has been adapted to microbes; the final talk was from Michael Gatzen about assessing batch effects for variants generated by two different pipelines.

Workflow Management Systems are always a popular topic at BOSC, and this year was no exception. This session included updates on widely used workflow systems such as Nextflow, Dockstore and Sapporo, and introductions to newer resources such as WARP and WFPM.

A short session on visualization tools and platforms focused on the venerable genome browser, JBrowse, now deployable through Docker and with a major update. It also introduced GO-Figure!, a new viz tool for Gene Ontology terms. The final session of BOSC, Translational Bioinformatics, included hot topics such as knowledge graphs and drug discovery, all in an open source context.

BOSC Chair Nomi Harris ended the day by thanking the many people who helped to make BOSC 2021 possible, including the organizers, reviewers, sponsors, and presenters. We look forward to seeing everyone (hopefully in person) at BOSC 2022!

VarI
VarI COSI’s second day at ISMB ECCB 2021 started with a keynote presentation titled “Mutate everything” by Ben Lehner from the (Centre for Genomic Regulation, Barcelona). Ben presented recent work on mutational scanning of protein coding genes allowing to quantify mutations’ effects on protein folding, binding and aggregation as well as to characterize protein free energy changes for the identification of allosteric sites. Mutational scanning was also a main topic of the round table discussion moderated by Yana Bromberg (Rutger University) with Douglas Fowler (University of Washington), Daniel Gilchrist (NHGRI) and Predrag Radivojac (Northeastern University), where current challenges on variant annotation and interpretation were addressed. Adding to the round table, a total of 7 selected talks were presented with a major focus on clinical interpretation of human variants from sequencing studies, covering a broad range of aspects such as the structural and mutational features of pathogenic variants, the interpretation of Copy Number Variants, and the characterization of gain-of-function variants. The session included a presentation from Variantyx, VarI COSI’s main sponsor, where Alexander Kaplun presented recent computational developments for variant calling in non-uniquely mappable regions from short-read WGS data.

iRNA
The third and last day of the 2021 iRNA COSI had an emphasis on RNA structure/RNA interactions/RNA quantification using long reads and featured two fascinating keynotes. Yue Wan discussed mapping of RNA-RNA interactions with applications illustrated in the analysis of SARS-CoV-2 while Liang Huang talked about the prediction of RNA secondary structure, with interesting historical considerations and comparisons across fields, finishing with the important application of their linear tool to SARS-CoV-2. Contributed talks discussed the transcriptomics analysis of a lncRNA, a snoRNA and a miRNA network as well as important considerations in the analysis of long read and direct RNA sequencing. In addition, the community heard about two challenges started within the context of the RNA society meeting with calls for participation. Overall, the 2021 iRNA COSI was very successful with varied aspects of computational RNA research explored, a timely live panel discussion, fascinating keynotes and enthusiastic poster presentations.

Thank you to our Exhibitors!

 

Thank you to our generous sponsors!

 



Harvard Medical School Department of Biomedical Informatics

See you next year in-person at ISMB 2022!

 

 
 

 
 

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, Highlights & Recap!

ISMB/ECCB 2021

 

Day 5: Highlights & Recap!

 

With only one day left, ISMB/ECCB 2021 gave us a day starting off with Exhibitor Demos from EMBL-EBI, PerMedCoE, and GOBLET. The day continued into 9 different COSI tracks, including one for General Computational Biology, and a Special Session Final Project Presentations: Collaborative Tools for Protein Analysis Hackathon 2021.

Highlights
ISCB Innovator Award Keynote, Ben Raphael gave an engaging talk on Quantifying Tumor Heterogeneity across Time and Space. Tumors are heterogeneous mixtures of normal and cancerous cells with distinct genetic and transcriptional profiles. In this talk, he presented present several computational approaches to quantify tumor heterogeneity and to study tumor evolution using single-cell and spatial sequencing technologies. For single-cell DNA sequencing data, he described algorithms to reconstruct tumor evolution from multiple types of somatic mutations and how to use these approaches to analyze changes in tumor genomes over time. For spatial transcriptomics data, he introduced algorithms to detect genomic aberrations and to align and integrate data from multiple adjacent tissue sections leveraging both spatial and transcriptional similarity. The applications of these methods to quantify spatial heterogeneity in several cancer types were illustrated.



 

*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

BOSC

BOSC 2021 (https://www.open-bio.org/events/bosc-2021/), the 22nd annual Bioinformatics Open Source Conference, kicked off this morning with opening remarks by BOSC Chair Nomi Harris, speaking from her home in California at 4:00am local time. The opening session also included an overview of the Open Bioinformatics Foundation by OBF President Peter Cock.

The first BOSC 2021 keynote talk, “Significant heterogeneities: Ecology’s emergence as open and synthetic science”, was delivered live by Christie Bahlai. Ecology has not been a big topic at past BOSCs, but Christie’s approach to open and inclusive science strongly resonated with our community. One attendee commented, “Christie Bahlai's keynote was inspiring and a breath of fresh air. +1 to calling out open science purists and the call for collective responsibility.”

Christie’s keynote was followed by a session on Standards and Practices for Open Science. One speaker in that session, Dhrithi Deshpande, spoke about the disappointingly low percentage of scientific papers that provide a link to the code (only about 12% -- though up from only 1% in 2016!), and noted that articles that share code tend to get cited more.

The next session, Tools for Open Science, started off with a well-received talk by Thorin Tabor about GenePattern, a reproducible research platform built on top of Jupyter Notebook.

Today’s final BOSC session was a joint session with Function COSI, chaired by Iddo Friedberg, featuring a keynote talk by Lara Mangravite on “Open approaches to advance data-intensive biomedicine.” 210 participants attended this joint session. Lara noted that clinical applications need access to high-quality data, but broad accessibility of human clinical data is difficult due to privacy issues, and access to analysis capabilities is distributed inequitably and tends to leave out those in the global south. Lara discussed some possible mitigations for those challenges.

Birds of a Feather, which bring together participants to chat informally about a shared interest, are always a popular feature of ISMB. In the BoF “Next steps for computational reproducibility toward fully executable papers”, there were discussions around ‘What is reproducibility?” and how do we incentivize new PIs to make reproducible work? Some cloud frameworks like Terra allow for reproducibility and lower the barrier for those who don’t have computational infrastructure in house. On the other hand, what about cloud costs? And is the reason why more papers aren’t reproducible the lack of skilled software engineers on the team?

The day ended with a hangout in the BOSC roundtable (which quickly ran into the 16-person maximum) that evolved into a discussion of the OBF and new ways for it to serve the open source bioinformatics community.

Don’t miss the second and final day of BOSC 2021 tomorrow, which begins with the last of our three keynotes, Thomas Hervé Mboa Nkoudou speaking about “Contribution of the maker movement to biotechnology in Africa: An open science perspective” (in French with English subtitles).

CAMDA

The 2nd day of virtual CAMDA 2021 started with an exceptional talk by Weida Tong, director of the Division of Bioinformatics and Biostatistics at the NCTR of the US FDA. Dr Tong discussed five common myths about AI and their implications for regulatory science, and provided a broad overview of how the FDA uses AI/ML techniques in support of the prediction of Drug Induced Liver Injury (DILI). This was followed by further presentations employing a variety of 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 seond half of the day was devoted to the Metagenomic Phage Forensics of Anti-Microbial Resistance challenge based on recently published MetaSUB Consortium data, which was explored by the CAMDA community this year for the first time, yielding novel complex relationships between phages and AMR that indicated a new for further investigations. The rich world of modern meta genomic data was then brilliantly characterised in our keynote by Nikos Kyrpides from the DOE Joint Genome Institute, ranging from the Earth microbiome to the Global virome.

Join us on Friday for an introduction to Disease Maps for modelling COVID-19 by Maria Peña Chilet of the FPS in Seville, followed by contributed talks of the matching data analysis challenge. In the next session we host ISMB/ECCB proceedings presentations on using AI/ML in cancer studies as well as AI-driven Cloud Laboratories. We will wrap up the day with the CAMDA Cafe where the CAMDA community will discuss the Grand challenges of our times to tackle in the coming years, and finishing with the awards ceremony for the traditional CAMDA Trophy for the best presentation. Join us! See www.camda.info for details.

iRNA
The second day of the iRNA COSI 2021 was dominated by epitranscriptomics. The keynote was given by Kathi Zarnack from the Buchmann Institute for Molecular Life Sciences in Germany who discussed the detection/prediction of m6A RNA modifications using transcriptomics data and machine learning, identifying sites within consensus DRACH motifs but also others, providing a rich resource for further studies. Two contributed talks on splicing kinetics and modeling of multivalent binding by RNA-binding proteins were followed by five talks on RNA modification detection from sequencing, raising important common issues and challenges which were addressed in our live panel discussion, to which participated Nicole Martinez, Shengdong Ke and Schraga Schwartz. The panel highlighted the fact that while a decade ago, the challenge in epitranscriptomics was to determine where the modifications are, with rapid and considerable increases in technology capacity brought on by innovations in the field, we are now switching gears and focusing on questions like the function of the modifications, how to address the interconnectedness of the process and the effects throughout the life cycle of the targeted RNA, and the use of systematic perturbations and their analysis using machine learning to understand what the modifications are really doing in the cell. Our panel was followed by our second poster session and our traditional social time with quiz during which we took time to catch up and learned much trivia about the Olympics including surprising facts.

VarI
During the first day of the VarI meeting we had two keynote talks. Alessandra Carbone (Sorbonne University) presented her recent work on the analysis of evolutionary information for detecting protein sites in viral proteomes important for protein-protein interaction and drug resistance. Later, Ben Langmead (John Hopkins University) presented methods for reducing reference bias in the detection of human variations. The proposed approaches are based on new algorithms that allow to align sequencing reads to the reference genome of different populations. The VarI meeting also hosted a proceeding talk from Chirag Jain who presented a new approach for minimizing variation graph size that allows to reduce the computational complexity in the methods for reducing genome bias. In the first days the program included 6 selected presentations focusing on variant prioritization, sex dependent genotype association studies and pleiotropy. Finally, we had a poster session with 18 works presented.

Tomorrow we will have a keynote talk from Ben Lehner (Centre for Genomic Regulation) and a roundtable discussion with Yana Bromberg, (Rutger University), Douglas Fowler (University of Washington), Daniel Gilchrist (NHGRI) and Predrag Radivojac (Northeastern University). Alex Kaplun will present the research activity of Variantyx which has been our main sponsor in the last few years.

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

 
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.

 

Tomorrow, 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 
 
 
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, 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 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 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