11/14/15
NHLBI Progenitor Cell Biology Consortium (PCBC)
Bioinformatics Committee Conference Call
Wednesday, November 4, 2015, 4:00 PM - 5:00 PM (ET)
(3 PM – 4 PM, CT; 2 PM – 3 PM, MT; 1 PM – 2 PM, PT)
Summary Notes
Participants: Antonis Hatzopoulos (Chair), Bruce Aronow, Jeffrey Huo, James Luo, Larsson Omberg,
Nathan Salomonis, Shannon Sui, Lynn Schriml, Ling Tang, Michael Terrin, John Thomas
Action Items
 Manuscript Updates (Bruce Aronow, Carolyn Lutzko, Nathan Salomonis)
o In order to address the questions raised by editors from Stem Cell Reports sufficiently; the
group will speak with the editors first to address their concerns before resubmission of
manuscript #1.
o

Larsson Omberg reported that the analysis is progressing for manuscript #2. They expect
that a draft of this differentiation manuscript will be available for review within a few weeks.
Bioinformatics Core/Synapse
o Nathan Salomonis will include a comprehensive list of collaboration efforts in the progress
report.
o
Group plans to advertise the tools and resources in Synapse at the next ISSCR meeting
(June 2016 in San Francisco).
o
Group plans on adding help desk hours to assist users.

Bioinformatics Training
o Nathan Salomonis and Larsson Omberg will discuss this training proposal with the Skills
Development Committee first before submission.

Other Business
o Antonis Hatzopoulos recommended the group to think about a possible application that
may fit the scope of this core to continue the work in the PCTC or an R01.
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1. Opening Remarks and Minutes of the September 24, 2015, Conference Call
 Antonis Hatzopoulos welcomed the committee members and minutes were accepted as is.
2. Feedback on the 7th Annual PCBC Meeting, Houston, TX
 Main Meeting Presentations
o Nathan Salomonis reported that there was more excitement from the attendees at the
Fellows Only Session than the main meeting in response to the available bioinformatics
resources presented. Some attendees commented that they were not aware that there
was a bioinformatics training course offered in late September. If there is another
bioinformatics training opportunity in the future, they are interested in attending.
 Bioinformatics Booth
o Nathan Salomonis and Larsson Omberg reported that the bioinformatics booth was
useful for some attendees. With their help, a few investigators have started on analyzing
their own datasets using the available tools and resources provided.
o
Michael Terrin recommended that the core to track the collaboration efforts and present
this aggregated data in the progress report.
o
Nathan Salomonis will include a comprehensive list of collaboration efforts in the
progress report.
 Steering Committee Meeting
o Larsson Omberg reported that there was a misunderstanding that the September
bioinformatics training course was under-subscribed. In fact, the course was fully
subscribed with 17 trainees.
o
Nathan Salomonis and Larsson Omberg are interested in putting together another
course. Michael Terrin encouraged them to submit a course proposal to be funded under
this year’s funding.
o
Nathan Salomonis and Larsson Omberg will discuss this training proposal with the Skills
Development Committee first before submission.
3. Manuscript Updates (Bruce Aronow, Carolyn Lutzko, Nathan Salomonis)


Manuscript 1, “A Comprehensive Resource for Characterizing Diverse Human Pluripotent
Stem Cell Lines”
o
Nathan Salomonis reported Carolyn Lutzko has been working with the histology control
lab on some follow up analysis and other edits.
o
In order to address the questions raised by the editors from Stem Cell Reports
sufficiently; the group will speak with the editors first to address their concerns before
resubmission.
o
Anticipate resubmitting manuscript before the end of the year.
Second Manuscript
o

Larsson Omberg reported that the analysis is progressing. They expect that a draft of
this differentiation manuscript will be available for review within a few weeks.
Bioinformatics Core
o Synapse: Metrics and Activities (Larsson Omberg, Kenny Daily)
o
Kenneth Daily reported an increase in usage of Synapse during training course
and investigators meeting periods.
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o
Group plans to advertise the tools and resources in Synapse at the next ISSCR
meeting (June 2016 in San Francisco).
o
Group plans on adding help desk hours to assist users.
4. Cell Characterization Core and Bioinformatics (Carolyn Lutzko)
 Disease Origin Cell Lines Update – tabled for next call

WiCell Update – tabled for next call
5. Bioinformatics Training (Larsson Omberg, Nathan Salomonis)

Trainings/Webinars
o
Upcoming Trainings/Webinars
o
17 trainees registered for the “Introduction to Bioinformatics and Computational
Genomics for Stem Cell Biologists” course at Montana State from September 28,
2015 – October 1, 2015. Overall, the evaluations on the course are very positive
with some room for improvements. Data and tools were relevant to the attendees
and they expressed recommending the course to their laboratory colleagues.
o
For future course, consider to having two different parallel training tracks (one
with more advance content and one on the basics).
6. Other Business

Antonis Hatzopoulos recommended the group to think about a possible application that may fit
the scope of this core to continue the work in the PCTC or an R01.
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