September 2019 HuBMAP All-Hands Meeting
Stanford University
List of Attendees
| First Name | Last Name | Funded project | Role | |
|---|---|---|---|---|
| Sushma Anand | Akoju | sushma.ananda13@gmail.com | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | External Program Consultants |
| Yousef | Al-Kofahi | alkofahi@ge.com | Rapid Technology Implementation | PI |
| Mark | Atkinson | atkinson@ufl.edu | TMC: Florida (Atkinson, Bodenmiller, Nick) | PI |
| Amir | Bahmani | abahman@stanford.edu | TMC: Stanford (Snyder) | Other |
| Ziv | Bar-Joseph | zivbj@cs.cmu.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | PI |
| Winston | Becker | wbecker@stanford.edu | TMC: Stanford (Snyder) | Graduate Student |
| Tyler | Best | tyler.best@nih.gov | Not Applicable | NIH Staff |
| Philip | Blood | blood@psc.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Katy | Borner | katy@indiana.edu | HIVE: IU (Borner) | PI |
| Annemarie | Boss | annemarie.boss@knowinnovation.com | Not Applicable | External Program Consultants |
| Maigan | Brusko | maigan@ufl.edu | TMC: Florida (Atkinson, Bodenmiller, Nick) | Other |
| Andreas | Bueckle | abueckle@indiana.edu | HIVE: IU (Borner) | Graduate Student |
| Kristin | Burnum-Johnson | kristin.burnum-johnson@pnnl.gov | TTD: Purdue (Laskin) | Other |
| Louise | Cabansay | lcabansa@ucsc.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | Other |
| Long | Cai | longcai@gmail.com | TTD: Caltech-Harvard (Cai, Yuan) | PI |
| Jeannie | Camarillo | jeannie.camarillo@northwestern.edu | Rapid Technology Implementation | Postdoc |
| Hassan | Chaib | hchaib@stanford.edu | TMC: Stanford (Snyder) | Other |
| Marc | Charette | marc.charette@nih.gov | TTD: Caltech-Harvard (Cai, Yuan) | NIH Staff |
| Fei | Chen | chenf@broadinstitute.org | Rapid Technology Implementation | PI |
| Mike | Cherry | cherry@stanford.edu | TMC: Stanford (Snyder) | Guests |
| Roxanne | Chiu | rbchiu@stanford.edu | TMC: Stanford (Snyder) | Technician |
| Richard | Conroy | conroyri@mail.nih.gov | Not Applicable | NIH Staff |
| Leonard | Cross | lecross@iu.edu | HIVE: IU (Borner) | Other |
| Seth | Currlin | scurrlin@ufl.edu | TMC: Florida (Atkinson, Bodenmiller, Nick) | Graduate Student |
| Nina | Dar | ninadar@caltech.edu | TTD: Caltech-Harvard (Cai, Yuan) | Technician |
| Ron | Davis | krhong@stanford.edu | Not Applicable | Guests |
| Stephen | Deems | deems@psc.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Tushar | Desai | tusharjd00@gmail.com | TTD: Stanford (Harbury, Desai) | PI |
| Michelle | Devlin | mdevlin@psc.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Timothy | Dunne | tim.dunne@knowinnovation.com | Not Applicable | Other |
| Elizabeth | Duong | taduong@ucsd.edu | TMC: UCSD (Zhang, Hagood, Jain, Kharchenko, Sun) | Postdoc |
| Ed | Esplin | explain@stanford.edu | TMC: Stanford (Snyder) | Postdoc |
| Samouil | Farhi | sfarhi@broadinstitute.org | Rapid Technology Implementation | Other |
| Shane | Filus | filus@psc.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Zorina | Galis | zgalis@gmail.com | Not Applicable | NIH Staff |
| Deep | Ganguli | dganguli@chanzuckerberg.com | Not Applicable | Other |
| Nils | Gehlenborg | Nils@hms.harvard.edu | HIVE: Harvard (Gehlenborg) | PI |
| Ellen | Gelfand | egelfand@broadinstitute.org | Not Applicable | Guests |
| Zinaida | Good | zinaida@stanford.edu | TMC: Stanford (Snyder) | Postdoc |
| William | Greenleaf | wjg@stanford.edu | TMC: Stanford (Snyder) | PI |
| Fiona | Griffin | fiona.griffin@chanzuckerberg.com | Not Applicable | Guests |
| Tuhin | Guha | tuhin83@stanford.edu | TMC: Stanford (Snyder) | Postdoc |
| Danielle | Gutierrez | d.gutierrez@vanderbilt.edu | TMC: Vanderbilt (Caprioli, Spraggins) | Other |
| James | Hagood | jhagood@unc.edu | TMC: UCSD (Zhang, Hagood, Jain, Kharchenko, Sun) | PI |
| Ryan | Hammer | hammer.ryanw@gmail.com | Not Applicable | Other |
| Bruce | Herr | bherr@indiana.edu | HIVE: IU (Borner) | Technician |
| Stephen | Hewitt | hewitts@mail.nih.gov | Not Applicable | External Program Consultants |
| John | Hickey | jwhickey@stanford.edu | TMC: Stanford (Snyder) | Postdoc |
| Aaron | Horning | ahorning@stanford.edu | TMC: Stanford (Snyder) | Postdoc |
| Lucy | Hsu | lucy.hsu@nih.gov | Not Applicable | NIH Staff |
| Shannon | Hughes | shannon.hughes@nih.gov | Not Applicable | NIH Staff |
| Lihua | Jiang | lihuaj.s@gmail.com | TMC: Stanford (Snyder) | Other |
| Marda | Jorgensen | marda@ufl.edu | TMC: Florida (Atkinson, Bodenmiller, Nick) | Other |
| Peter | Kant | pkant@scivelo.pitt.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Maria | Keays | mk29@sanger.ac.uk | Not Applicable | Other |
| Neil | Kelleher | n-kelleher@northwestern.edu | Not Applicable | PI |
| Junhyong | Kim | junhyong@sas.upenn.edu | Not Applicable | External Program Consultants |
| Blue | Lake | b1lake@eng.ucsd.edu | TMC: UCSD (Zhang, Hagood, Jain, Kharchenko, Sun) | Other |
| Julia | Laskin | jlaskin@purdue.edu | TTD: Purdue (Laskin) | PI |
| Kevin | Leung | kevin.leung@ucsf.edu | Not Applicable | Other |
| Shin | Lin | shinlin@uw.edu | TMC: Caltech (Cai, Shendure, Trapnell) | Other |
| Beth | Lowry | lowrye2@uw.edu | Not Applicable | PI |
| Trevor | Manz | trevor.j.manz@gmail.com | HIVE: Harvard (Gehlenborg) | Graduate Student |
| Georgi | Marinov | marinovg@stanford.edu | TMC: Stanford (Snyder) | Postdoc |
| William | Mauck | wmauck@nygenome.org | HIVE: NYGC (Satija) | Other |
| Robert | Murphy | murphy@cmu.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | PI |
| Monica | Nagendran | nmonica@stanford.edu | TTD: Stanford (Harbury, Desai) | Postdoc |
| Elizabeth | Neumann | Elizabeth.neumann@vanderbilt.edu | TMC: Vanderbilt (Caprioli, Spraggins) | Postdoc |
| Stephanie | Nevins | snevins@stanford.edu | TMC: Stanford (Snyder) | Graduate Student |
| Harry | Nick | hnick@ufl.edu | TMC: Florida (Atkinson, Bodenmiller, Nick) | PI |
| Debra | Nigra | nigra@psc.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Nicholas | Nystrom | nystrom@psc.edu | HIVE: IEC (Nystrom, Silverstein) | PI |
| Brian | O'Connor | broconno@ucsc.edu | Not Applicable | Other |
| Charles | Overbeck | coverbec@ucsc.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | Other |
| Benedict | Paten | bpaten@ucsc.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | PI |
| Natalie | Perez | nperez9@ucsc.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | Other |
| Nico | Pierson | nicogpt@caltech.edu | TTD: Caltech-Harvard (Cai, Yuan) | Technician |
| Ajay | Pillai | ajay.pillai3@nih.gov | Not Applicable | NIH Staff |
| Sylvia | Plevritis | sylvia.plevritis@stanford.edu | TMC: Stanford (Snyder) | PI |
| Dena | Procaccini | dena.procaccini@nih.gov | Not Applicable | NIH Staff |
| Gloria | Pryhuber | gloria_pryhuber@urmc.rochester.edu | TMC: UCSD (Zhang, Hagood, Jain, Kharchenko, Sun) | Other |
| Donnalyn | Roxey | donnalyn.roxey@knowinnovation.com | Other | |
| Ananda L | Roy | ananda.roy@nih.gov | Not Applicable | NIH Staff |
| Matthew | Ruffalo | mruffalo@cs.cmu.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | Other |
| Sinem | Saka | sinem.saka@wyss.harvard.edu | TTD: Harvard (Yin) | Postdoc |
| Robin | Scibek | flaus@psc.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Walter | Shands | jshands@ucsc.edu | HIVE: CMU (Bar-Joseph, Paten, Teichmann) | Other |
| Kavya | Sharman | kavya.sharman@Vanderbilt.Edu | TMC: Vanderbilt (Caprioli, Spraggins) | Graduate Student |
| Jay | Shendure | shendure@uw.edu | TMC: Caltech (Cai, Shendure, Trapnell) | PI |
| Bill | Shirey | shirey@pitt.edu | HIVE: IEC (Nystrom, Silverstein) | Other |
| Jonathan | Silverstein | j.c.s@pitt.edu | HIVE: IEC (Nystrom, Silverstein) | PI |
| James | Sluka | jsluka@iu.edu | HIVE: IU (Borner) | Other |
| Michael | Snyder | mpsnyder@stanford.edu | TMC: Stanford (Snyder) | PI |
| Anup | Sood | anup.sood@ge.com | Rapid Technology Implementation | Other |
| Jeffrey | Spraggins | jeff.spraggins@vanderbilt.edu | TMC: Vanderbilt (Caprioli, Spraggins) | PI |
| Pothur | Srinivas | srinivap@mail.nih.gov | Not Applicable | NIH Staff |
| Courtney | Stockman | stockmca@stanford.edu | TTD: Stanford (Harbury, Desai) | Graduate Student |
| Tiancheng | Sun | tc.sun@nih.gov | Not Applicable | NIH Staff |
| Jason | Swedlow | j.r.swedlow@dundee.ac.uk | Not Applicable | PI |
| Norbert | Tavares | ntavares@chanzuckerberg.com | Not Applicable | Guests |
| Margaret | Vella | margaret_vella@hms.harvard.edu | HIVE: Harvard (Gehlenborg) | Other |
| Vishal Gautham | Venkataraaman | vgautham@stanford.edu | TMC: Stanford (Snyder) | Technician |
| Wendy | Wang | Wangw@mail.nih.gov | Rapid Technology Implementation | NIH Staff |
| Clive | Wasserfall | clive@ufl.edu | TMC: Florida (Atkinson, Bodenmiller, Nick) | PI |
| Griffin | Weber | weber@hms.harvard.edu | HIVE: IU (Borner) | Other |
| Bei | Wei | wbei@stnford.edu | TMC: Stanford (Snyder) | Postdoc |
| Jim | Wells | jim.wells@ucsf.edu | Not Applicable | PI |
| Dong Hye | Ye | donghye.ye@marquette.edu | TTD: Purdue (Laskin) | PI |
| Peng | Yin | py@hms.harvard.edu | TTD: Harvard (Yin) | PI |
| Kun | Zhang | kzhang@bioeng.ucsd.edu | TMC: UCSD (Zhang, Hagood, Jain, Kharchenko, Sun) | PI |
| Qian | Zhu | zqian@jimmy.harvard.edu | TTD: Caltech-Harvard (Cai, Yuan) | Postdoc |
Agenda
| Time | Session | Description | Slides or Notes |
|---|---|---|---|
| Monday, September 23 Goal Day 1: Review what has been achieved so far | |||
| 8:30 am | Welcome & Agenda | Donnalyn | |
| 8:40 am | Opening Remarks | Richard Conroy, Mike Snyder | |
| 9:00 am | Funded project updates (1-6) | Five minutes on: Your project Next year's deliverables Collaborations What should HuBMAP do? and five minutes on cool science | HIVE-IEC TMC-Stanford RTI-Stanford RTI-Broad TMC-Caltech TTD-Caltech |
| 10:03 am | Break | ||
| 10:33 am | Breakout 1: Funding Initiatives | HIVE - Tyler Best, Jonathan Silverstein TMCs - Mike Snyder and Zorina Galis TTDs - Peng Yin and Pothur Srinivas RTIs - Richard Conroy and Ananda Roy | HIVE - Tyler Best, Jonathan Silverstein TMCs - Mike Snyder and Zorina Galis TTDs - Peng Yin and Pothur Srinivas RTIs - Richard Conroy and Ananda Roy |
| 11:43 am | Funded project updates (7-9) | Five minutes on: your project next year's deliverables collaborations what should HuBMAP do? and five minutes on cool science | TMC-VU RTI-GE TTD-Harvard |
| 12:15 pm | Lunch | ||
| 1:05 pm | Funded project updates (10-12) | Five minutes on: Your project Next year's deliverables Collaborations What should HuBMAP do? and five minutes on cool science | RTI-NW TTD-Purdue TMC-UF |
| 1:47 pm | Collaborative Projects Round Robin | Suggested agenda: Introductions Progress during past year Plans for the upcoming year: please note if goals, milestones or personnel have changed Identify someone responsible for each proposed activity Any new collaborations proposed? | Notes from all collaborative projects Round Robin sessions are found in Google Drive here: https://drive.google.com/open?id=1nLyuspH00_Hzg6FUbNxw9ONtaKnjhcDj |
| Round1 | |||
| TMC-Caltech, TTD-Caltech & TMC-Stanford TMC-VU & TMC-UCSD TMC-UF, HIVE-CMU & HIVE-Harvard TTD-Stanford & RTI-GE TTD-Harvard, TTD-Purdue & RTI-NW HIVE-IEC & RTI-Stanford HIVE-NYGC, HIVE-Indiana & RTI-Broad |
|||
| Round2 | |||
| TMC-Caltech, TTD-Caltech & TMC-UF TMC-VU, TTD-Purdue & RTI-Stanford TMC-Stanford, HIVE-CMU & HIVE-Harvard TMC-UCSD & RTI-NW TTD-Harvard & TTD-Stanford HIVE-IEC & RTI-Broad HIVE-NYGC, HIVE-Indiana & RTI-GE |
|||
| Round 3 | |||
| TMC-Caltech, TTD-Caltech & TTD-Stanford TMC-VU, TMC-UF & RTI-NW TMC-UCSD, HIVE-CMU & HIVE-Harvard TTD-Purdue & RTI-Stanford TTD-Harvard & TMC-Stanford HIVE-IEC & RTI-GE HIVE-NYGC, HIVE-Indiana & RTI-Stanford |
|||
| 3:27 pm | Break | ||
| 3:57 pm | Funded Project updates (13-18) | Five minutes on: Your project Next year's deliverables Collaborations What should HuBMAP do? and five minutes on cool science | TMC-UCSD TTD-Stanford HIVE-CMU HIVE-Harvard HIVE-NYGC HIVE-IU |
| 5:00 pm | Adjourn | ||
| 5:05 pm | Posters, demos, and networking | Posters should be 3' x 4' | |
| Time | Session | Description | Slides or Notes |
|---|---|---|---|
| Tuesday September 24 Goal Day 2: Working group updates and outlining the roadmap for data releases | |||
| 8:35 am | Welcome & Agenda | ||
| 8:45 am | Opening - What are we hoping to achieve | Ajay & Jonathan | |
| 8:55 am | Working Group discussion | Policies - Gloria, Shin Comms & Engagement - Danielle, Robin TTDC - Clive, Long Data Science - Nils, Cole | Policies - Gloria, Shin Comms & Engagement - Danielle, Robin TTDC - Clive, Long Data Science - Nils, Cole |
| 10:10 am | Summarize and hear from working groups | Summaries from WG co-chairs | Policies No slides provided by other WGs |
| 10:55 am | Break & Group picture | ||
| 11:55 am | Data Release and Portal Team Orientation | Sequencing - Maigan/Matt Microscopy - Clive Mass Spec - Jeff Portal - Jonathan | Sequencing Microscopy Mass Spec Portal |
| 12:05 pm | Lunch | ||
| 1:05 pm | Data Release Team Breakouts - Session 1 | Suggested structure for breakouts | See Session 2 below for notes |
| 2:35 pm | Break | ||
| 3:05 pm | Report back | Four 12-minute presentations with feedback capture | Sequencing Microscopy Mass Spec |
| 4:05 pm | Data Release Team Breakouts - Session 2 | Sequencing - Maigan/Matt Microscopy - Clive Mass Spec - Jeff | Sequencing Microscopy Mass Spec |
| 5:05 pm | Wrap up day 2 | ||
| 5:10 pm | PI, PM, EPC & NIH meeting | A business meeting for NIH staff and PIs | NIH, EPC, PIs, PMs |
| 6:10 pm | A business meeting for NIH and External Program Consultants | NIH, EPCs | |
| 5:00 - 7:00 pm | Concurrent session: Early career activity | Open to all | |
| Time | Session | Description | Slides or Notes |
|---|---|---|---|
| Wednesday September 25 Goal Day 3: Explore collaborations with other programs in the broader research community | |||
| 8:30 am | EPC Remarks Welcome & Agenda | ||
| 8:45 am | Opening - What are we hoping to achieve | Plans for Communications and Engagement | Robin, Zorina, and Danielle |
| 8:55 am | What's going on with other consortia? | An opportunity to hear from 3 consortia about their goals, scope and participants | HCA / CZI - Nobert Tavares, Fiona Griffin SPARC - Tyler Best HTAN - Mike Snyder, Shannon Hughes |
| 9:55 am | Stewarding breakout topics for March meeting | ||
| 10:25 am | What's going on with other consortia? | An opportunity to hear from 3 consortia about their goals, scope and participants | BICCN - Kun Zhang KPMP - Sanjay Jain (remote) EuroBioimaging - Jason Swedlow |
| 10:55 am | Stewarding breakout topics for March meeting | ||
| 11:15 am | Break | ||
| 11:55am | Stewarding breakout topics for March meeting | ||
| 12:05pm | Adjourn & next steps | Set up next SC meeting, plans for the upcoming year... | |
| 12:05 pm | Meeting Ends, Lunch | ||
| 3:05 pm | Optional visits to Stanford labs | Visit to: Snyder, Harbury, Nolan, Angelo labs | Everyone who signed up! |