SDIWG:Ongoing Discussion 2011 - Revision history

Lysterp at 20:57, 22 December 2011

2011-12-22T20:57:56Z

Lysterp at 20:57, 22 December 2011

2011-12-22T20:57:03Z

Lysterp at 20:54, 22 December 2011

2011-12-22T20:54:32Z

Lysterp at 20:52, 22 December 2011

2011-12-22T20:52:21Z

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Rbaltman at 17:09, 20 November 2011

2011-11-20T17:09:46Z

Rbaltman at 02:36, 2 September 2011

2011-09-02T02:36:24Z

Rbaltman at 16:27, 30 August 2011

2011-08-30T16:27:03Z

Rbaltman at 16:26, 30 August 2011

2011-08-30T16:26:23Z

Lysterp at 01:49, 7 June 2011

2011-06-07T01:49:57Z

Lysterp at 01:37, 7 June 2011

2011-06-07T01:37:37Z

@@ Line 109: / Line 109: @@
 ACTION:  Russ will find dates for potential call in April/May and work with NIH staff and PIs to get agenda.
-==Tcon with PIs: Call Summary July 8, 2011==
+==Tcon with PIs July 8, 2011==
 Attendees:  Ivo Dinov (UCLA), Brian Athey (Michigan), Ron Kikinis (Harvard), Wendy Chapman (UCSD), Lucila Ohno-Machado (UCSD), Jim Cavalcoli (Michigan), Mark Musen (Stanford), Russ Altman (Stanford)

@@ Line 1: / Line 1: @@
 Meeting notes for NIH Roadmap National Centers for Biomedical Computing (NCBC) Centers to discuss plans for the last four years (2011-2015) of the NCBC effort
-The <b>most recent<\b> minutes and notes are at starting from the top-down in this document.
+The <b>most recent</b> minutes and notes are at starting from the top-down in this document.
-Link to [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group_(SDIWG)_and_Centers_Discussion NCBC Working Groups], and [http://na-mic.org/Wiki/index.php/SDIWG:Ongoing_Discussion discussions with PIs in 2004-2005]
+Link to Top Page of the NCBC wiki [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group_(SDIWG)_and_Centers_Discussion NCBC Working Groups], and [http://na-mic.org/Wiki/index.php/SDIWG:Ongoing_Discussion discussions with PIs in 2004-2005]
 Link to [http://www.ncbcs.org/summary.html The current list of NIH NCBC Project Team members and other information on the Centers Portal]
@@ Line 18: / Line 18: @@
 * In addition, the Project team would like for ideas/input from PIs for the next AHM/NCBCmeeting
-==Tcon with PIs November 9, 2011 ==
+==Tcon with PIs and Project Team November 9, 2011 ==
 NCBC PI & NIH Program Staff Conf Call
 November 9, 2011.   11-12 ET
-Attending:  Valerie Florance, Ray Fergerson, Peter Goode, Ron Kikinis, Lucila Ohno-Machado, Wendy Chapman, Suzanne Churchill, Andrea Califano, Ari Floratos, Tina Kapur,  Jim Cavalcoli, Peter Lyster, Heidi Sophia, Joy Ku, Karen Skinner, Michael Ackerman, Zak Kohane, Jennifer Villani, Grace Peng, Russ Altman.
+Attending:  Valerie Florance, Ray Fergerson, Peter Good, Ron Kikinis, Lucila Ohno-Machado, Wendy Chapman, Suzanne Churchill, Andrea Califano, Ari Floratos, Tina Kapur,  Jim Cavalcoli, Peter Lyster, Heidi Sophia, Joy Ku, Karen Skinner, Michael Ackerman, Zak Kohane, Jennifer Villani, Grace Peng, Russ Altman.
@@ Line 109: / Line 109: @@
 ACTION:  Russ will find dates for potential call in April/May and work with NIH staff and PIs to get agenda.
-==NCBC PI Call Summary July 8, 2011==
+==Tcon with PIs: Call Summary July 8, 2011==
 Attendees:  Ivo Dinov (UCLA), Brian Athey (Michigan), Ron Kikinis (Harvard), Wendy Chapman (UCSD), Lucila Ohno-Machado (UCSD), Jim Cavalcoli (Michigan), Mark Musen (Stanford), Russ Altman (Stanford)
@@ Line 176: / Line 176: @@
 *  Planning (or debrief) for AMIA panel
-== Tcon with PIs May 23 2011 ==
+== Tcon with PIs and Project Team May 23 2011 ==
 Present: PIs and their representatives; members of NCBC Project Team

@@ Line 109: / Line 109: @@
 ACTION:  Russ will find dates for potential call in April/May and work with NIH staff and PIs to get agenda.
-==NCBC PI Call Summary 7/8/11==
+==NCBC PI Call Summary July 8, 2011==
------------------------
 Attendees:  Ivo Dinov (UCLA), Brian Athey (Michigan), Ron Kikinis (Harvard), Wendy Chapman (UCSD), Lucila Ohno-Machado (UCSD), Jim Cavalcoli (Michigan), Mark Musen (Stanford), Russ Altman (Stanford)
@@ Line 178: / Line 177: @@
 == Tcon with PIs May 23 2011 ==
 Present: PIs and their representatives; members of NCBC Project Team

← Older revision		Revision as of 17:09, 20 November 2011
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	* In addition, the Project team would like for ideas/input from PIs for the next AHM/NCBCmeeting		* In addition, the Project team would like for ideas/input from PIs for the next AHM/NCBCmeeting
		+
		+	==Tcon with PIs November 9, 2011 ==
		+
		+	NCBC PI & NIH Program Staff Conf Call
		+	November 9, 2011. 11-12 ET
		+
		+	Attending: Valerie Florance, Ray Fergerson, Peter Goode, Ron Kikinis, Lucila Ohno-Machado, Wendy Chapman, Suzanne Churchill, Andrea Califano, Ari Floratos, Tina Kapur, Jim Cavalcoli, Peter Lyster, Heidi Sophia, Joy Ku, Karen Skinner, Michael Ackerman, Zak Kohane, Jennifer Villani, Grace Peng, Russ Altman.
		+
		+
		+	1. Summary of status of JAMIA Special Issue. (Lucila Ohno-Machado)
		+
		+	All centers have papers submitted and accepted. There is a 12/15 deadline for an additional editorial that could then be included in the hardcopy March issue.
		+	If NIH staff is not able to do this, then we may want to ask Jeremy Berg and David Botstein (both private citizens, not NIH employees now) to consider editorial(s) about the NCBC program.
		+
		+	Lucila: the articles are available 'online first' at www.jamia.org (I am still working on making them free access, so you will have to vpn through your institution to access them from home, I am adding them to a dropbox for convenience and inviting all in this list, except NIH officers as I am not sure you are allowed to sign up using NIH email, let me know — one article still coming up due to some last minute corrections in the proofs, stay tuned). Authors can share personal copies for education and research purposes. Everyone can start citing these articles now, although they will likely be assigned to the March issue of JAMIA if we can get the editorial by Dec 15, or June if later. Thanks to all who helped make this happen, let me know if you have any questions.
		+
		+	ACTION: Lucila will assess likelihood that NIH staff will submit for 12/15. Otherwise, approach Berg & Botstein (with assistance as needed) to solicit editorials.
		+
		+	2. Do we want to do a special issue of another journal? Which one? Who will lead? (Russ Altman)
		+
		+	Lucila pointed out that perhaps better first to widely disseminate the JAMIA special writeups, particularly when they are all posted on the web. Some pointed out that the imaging community might be interested in a focused set of articles discussing the shared NCBC themes in imaging.
		+
		+	ACTION: Refer to JAMIA special issue liberally in talks, websites, and get people to read these!
		+
		+	2B. Special issue of Biomedical Computation Review targeted to NIH staff (Russ Altman/Peter Lyster)
		+
		+	This would cost approximately $25K = $3200K/center. The goal might be to trumpet NCBC achievements. There was skepticism about the value of this among some. Probably not sufficient interest to warrant this, unless a more clear reason emerges to do this.
		+
		+	ACTION: On Hold
		+
		+	3. Potential ISMB special session (Peter Lyster)
		+
		+	Peter has proposed to ISMB a special session in Long Beach for NCBC Centers. Interested centers should reserve July 14-16. Peter will alert PIs to outcome of proposal.
		+
		+	ACTION: Reserve July 14-16, 2012 in Long Beach for panel participation.
		+
		+	4. NCBC BISTI Symposium September 2012 (Peter Lyster)
		+
		+	There was a lively discussion about the value of a public symposium trumpeting the achievements of the NCBC program. There was, however, more general enthusiasm for a closed session of NCBC PIs and NIH program staff with NIH leaders, with a 1-2 hour roundtable discussion of the NCBC successes, and how to protect the NCBC investment in the coming years. It was proposed that perhaps a 1/2-3/4 day symposium could then end and a closed session with "thought leaders" (some of whom may elect to attend the symposium beforehand) per above. Potential thought leaders: Francis Collins, Harold Varmus, Eric Green, Ed Harlow, Don Lindberg, ACD rep, etc...
		+
		+	ACTION: NIH staff and NCBC PIs to decide on dates and potential format for symposium and/or thought leader discussion.
		+
		+	5. Report of NCBCs.org<http://NCBCs.org> ad hoc committee (Russ Altman, Jim Cavalcoli, Brian Athey)
		+
		+	A mockup of new site was distributed. Comments and suggestions welcome. NCBCs.org site will be updated by committee in next several months.
		+
		+	ACTION: Send comments/ideas to Jim Cavalcoli, Brian Athey, Russ Altman or Peter Lyster for improvements to website. This is not a funded project so content and ease of understanding are key vs. flash and complex functionality.
		+
		+	6. Biositemaps update/discussion (Ray Fergerson for Mark Musen)
		+
		+	Ray Fergerson provided the following update: We request that NCBC’s quarterly update their resource descriptions. This request went out last week and most have either already done so or promised to do so in the next couple weeks. We are following up with the rest.
		+
		+	There is an ongoing discussion about reimplementing the Biositemaps Resource Discovery System (RDS) in Drupal for both efficiency and portability. There was a collaborating RO1 proposal with NCBO from Pittsburgh and Duke to do this and secure solid funding for the project. Unfortunately this proposal was not funded. The lack of funding for the engineering effort means that progress on any major or minor changes to RDS happens irregularly and is not predictable or manageable. The team still continues to meet both internally and with external groups (NIF, CTSA's, Eagle-I). One critical area of focus is obviously additional possibilities for funding. Nothing identified yet.
		+
		+	Peter Lyster adds: Biositemaps, the Pittsburgh team plans to continue development, optimization, and improvement of the RDS query tool using new Drupal content management system.
		+
		+	7. What the program wants from NCBC program and PIs going into next year (Peter Lyster)
		+
		+	This discussion resolved primarily around the best way for NCBC program to engage thought leaders (per above) in order to make the case that NCBC activities need to be continued in some form after end of NCBC program.
		+
		+	8. Reporting formats for NCBC annual reports (Peter Lyster)
		+
		+	We did not discuss this item extensively, but NCBCs can expect a document from NIH with suggested (or mandated) categories for annual report metrics, in order to have a more standard method for reporting. The current document (circulated earlier) has elements from P41 center annual reports and systems biology annual reports.
		+
		+	ACTION: NIH staff will followup as they see fit with PIs. Comments on circulated document to Peter Lyster.
		+
		+	9. Public Private Partnerships? (Peter Lyster)
		+
		+	Brian Athey commented on a number of ongoing activities which NCBC PIs may want to engage in:
		+
		+	There are 3 OSTP RFIs that should be of interest to NCBC PIs. The first one is related to the creation of Public Private Partnerships (PPPs). We should really consider responding to this one. The others are of interest as well. They are all listed below:
		+
		+	1. Bioeconomy RFI http://www.whitehouse.gov/blog/2011/10/12/building-bioeconomy.
		+
		+	The National Bioeconomy Blueprint will highlight Administration progress in this productive and promising scientific and economic arena andidentify needs and goals, including:
		+	strategies to meet grand challenges in lean budget times;
		+	commercialization and entrepreneurship opportunities to open new markets;
		+	research and development investments in areas that will provide the foundation for the bioeconomy;
		+	enhancements of workforce training to prepare the next generation of scientists and engineers for the bioeconomy jobs of the future;
		+	regulatory reforms that will reduce unnecessary burdens and impediments while protecting health and safety, and
		+	bioeconomy public-private partnerships to accelerate innovation in key areas.
		+
		+	2. This one focuses on Public Access to Digital Data Resulting From Federally Funded Scientific Research – “to provide recommendations on approaches for ensuring long-term stewardship and encouraging broad public access to unclassified digital data that result from federally funded scientific research.” Responses to 13 questions are sought and cover issues of cost, credit, and mechanisms for preservation, discoverability, and access as well as standards for interoperability, re-use, and re-purposing. The due date is January 12, 2012.
		+	Data: http://federalregister.gov/a/2011-28621
		+
		+	3. This one is focused on Public Access to Peer-Reviewed Scholarly Publications Resulting From Federally Funded Research – “to provide recommendations on approaches for ensuring long-term stewardship and broad public access to the peer-reviewed scholarly publications that result from federally funded scientific research.” Responses to 8 questions are sought and cover economic growth impact; intellectual property interests; centralized versus de-centralized approaches; public-private partnerships; interoperable search, required metadata, accessibility; burden; range of publications covered; and embargo period. The due date is January 2, 2012.
		+	Publications: http://federalregister.gov/a/2011-28623
		+
		+	10. Next call. We didn't specifically discuss this, but it seems to me that something in late winter, early spring would be appropriate.
		+
		+	ACTION: Russ will find dates for potential call in April/May and work with NIH staff and PIs to get agenda.
		+

	== Tcon with PIs May 23 2011 ==		== Tcon with PIs May 23 2011 ==

@@ Line 285: / Line 285: @@
 Mark Musen reported that Biositemaps has challenges because of multiple leadership and ownership issues from several groups devoted to it, including folks at Pittsburgh, Duke.  NCBC centers at Michigan, Stanford also engaged.  In addition, Wendy Chapman reported that the new UCSD NCBC was looking at different technology for this functionality, ORBIT, as part of an AMIA working group.  There may also be related efforts from the informatics groups within the CTSA centers.
-ACTION:  Musen lead an effort to advise NCBC PIs if/how biositemaps standards should be used, migrated to another standard, or other based on investigation of status and options.   NCBCs.org subcommittee will then consider how to update existing biositemaps-based listing of resources, in light of this advice.
+ACTION:  Musen to assist iDASH in adapting BioSitemaps for resource documentation.  All NCBCs to ensure that BioSitemaps descriptions are up to date.  NCBO will assist as necessary.
 .  Targeting other NIH programs to which we should link individually or as a group

@@ Line 253: / Line 253: @@
 .	What can be done with existing opportunities http://www.bisti.nih.gov/funding/index.asp.   NIH need to try to grow this, and it is cyclic activity with dynamic input from NCBCs, e.g., joint outreach to get more PIs to respond to Collaboration R01/R21 etc. Program Projects.  BISTI R01s PAR 09 218.  Unsolicited R01s etc.
 ==NCBC PI Call Summary 7/8/11==
@@ Line 331: / Line 322: @@
 *  Planning (or debrief) for AMIA panel
 ==Appendix B: Original charter of SDI (software and data integration): Charter of SDI: ==

← Older revision		Revision as of 16:26, 30 August 2011
Line 262:		Line 262:

	Can be found at http://www.ncbcs.org/summary.html		Can be found at http://www.ncbcs.org/summary.html
		+
		+	==NCBC PI Call Summary 7/8/11==
		+	-----------------------
		+	Summary of NCBC PI Phone Call 7/8/11
		+	Attendees: Ivo Dinov (UCLA), Brian Athey (Michigan), Ron Kikinis (Harvard), Wendy Chapman (UCSD), Lucila Ohno-Machado (UCSD), Jim Cavalcoli (Michigan), Mark Musen (Stanford), Russ Altman (Stanford)
		+
		+	[NOTE: communication error meant i2b2 and Magnet alternate reps not given call-in information.]
		+
		+	AGENDA, summary of discussion, and action items
		+
		+	Russ began discussion stressing need for PIs to engage in appropriate "Big P" activities for the last few years of the NCBC program for multiple reasons. One proposed goal would be for the PIs to author (for NIH staff use and information) a brief ~2 page annual summary of "Big P" activities and goals. The contents of this meeting will form the basis for the first report.
		+
		+	1. Updating NCBCs.org to better reflect our activities
		+
		+	We agreed that keeping the website up to date is critical. There are a few opportunities for updating and adding content.
		+
		+	ACTION: Brian, Jim and Russ will form an ad hoc subcommittee to request information and add data to this site. This will include adding or updating the following:
		+	* contact info
		+	* URL for access to resources for each site "Access our resources." Important to recognize that resources can be software, data, models, or web-based portals/applications or combinations of these.
		+	* exhaustive list of collaborating sites with all NCBCs
		+	* The group should also check web logs for NCBCs.org and see what kind of traffic it gets
		+	* The group should also encourage NCBCs to link back to this page on their center pages, and to mention the site in talks, papers.
		+
		+
		+	2. Making sure that each Center has a long term archival plan for distributing software, even after NCBC program ends
		+
		+	ACTION: NCBCs.org subcommittee will ask each center for a statement about their long term archival plans to ensure that the resources referenced above are available after the NCBC grant period. It will also be useful to know if there are any plans for long term maintenance/extension of these resources, realistically speaking.
		+
		+	3. Publicizing our software releases to the community, keeping biositemaps up to date
		+
		+	Mark Musen reported that Biositemaps has challenges because of multiple leadership and ownership issues from several groups devoted to it, including folks at Pittsburgh, Duke. NCBC centers at Michigan, Stanford also engaged. In addition, Wendy Chapman reported that the new UCSD NCBC was looking at different technology for this functionality, ORBIT, as part of an AMIA working group. There may also be related efforts from the informatics groups within the CTSA centers.
		+
		+	ACTION: Musen lead an effort to advise NCBC PIs if/how biositemaps standards should be used, migrated to another standard, or other based on investigation of status and options. NCBCs.org subcommittee will then consider how to update existing biositemaps-based listing of resources, in light of this advice.
		+
		+	4. Targeting other NIH programs to which we should link individually or as a group
		+
		+	The P41 program of the former NCRR (most of which is moving to NIGMS) represents a set of centers that may be appropriate for many of the NCBCs to interact with.
		+
		+	5. NIH staff has asked for a list of all collaborators and subcontracts, so we can ask them to link their webpages back to ncbcs.org
		+
		+	ACTION: NCBCs.org subcommittee will request this information and gather it together and post on site.
		+
		+	6. NIH staff has asked for a common format for progress reports in terms of metrics (papers, web hits, training numbers, software downloads, collaborations, popular press mentions?
		+
		+	The systems biology grants have created a document suggesting metrics that may be appropriate for measuring progress and impact of centers. This document has been shared in DRAFT form (attached, PLEASE DO NOT DISTRIBUTE FURTHER UNTIL FINALIZED) by Bodo Stern and Peter Sorger from that group.
		+
		+	ACTION: Distribute to PIs and discuss pros/cons of using these in our annual reports on the next phone call.
		+
		+
		+	7. Status report on JAMIA special issue. Do we need another forum for reporting to other communities?
		+
		+	We agreed that parallel or joint papers on a regular basis in a variety of forums is very valuable. There was a sense that we should complete these serially (i.e. get the JAMIA papers out first, then consider next target), and so we will discuss next steps after the JAMIA submissions are completed. Also will avoid fatigue.
		+
		+	ACTION: Submit to JAMIA by July 13 deadline (goal: all centers submit). Discuss at next call the next best joint publication activity and its appropriate timing.
		+
		+	8. Conference presentation (AMIA panel approved).
		+
		+	ACTION: Brian Athey to poll PIs for possible participation in this panel, by sending date and asking for availability.
		+
		+	9. OTHER
		+
		+	ACTION: Russ to schedule next PI phone call in 3-4 months. NIH staff will be invited as well. Before that will draft an annual report based on the outcomes of the activities above. Preliminary agenda for next phone call:
		+
		+	* Review of updated NCBCs.org (subcomm)
		+	* Discussion of Biositemaps status (Musen)
		+	* Discussion of Systems Biology metrics and addition/subtraction +/- adoption of a strategy for reporting among NCBCs.
		+	* Discussion of next step in joint publication strategy
		+	* Planning (or debrief) for AMIA panel
		+

	==Appendix B: Original charter of SDI (software and data integration): Charter of SDI: ==		==Appendix B: Original charter of SDI (software and data integration): Charter of SDI: ==

← Older revision		Revision as of 01:49, 7 June 2011
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	* Establishing common format for reporting (web hits, usage of software, training). This item arose out of other discussions between participants.		* Establishing common format for reporting (web hits, usage of software, training). This item arose out of other discussions between participants.
		+
		+	* NIH staff will get some statistics on the funded awards in the area of Biomedical Informatics and Computational Biology (BICB) as well as the current complement of Computational P41s. Note that there is an editorial in Biomedical Computational Review last year that summarizes the current state of NIH funding in BICB as well as the study sections that review applications for BICB: http://www.biomedicalcomputationreview.org/6/2/9.pdf

	== Tcon on February 2 with Kikinis NA-MIC team ==		== Tcon on February 2 with Kikinis NA-MIC team ==

@@ Line 25: / Line 25: @@
 * Collective Paper(s): Lucila Ohno-Machado (iDASH) is taking a lead
-* Improving the Internet profile of the NCBC program: Maintaining http://www.ncbcs.org/, ensuring that all affilitated institutions (subcontracts, DBPs, collaborating R01/R21s) link to this site.  http://www.biositemaps.org/ continuing the maintenance of this and using it to maximize the Internet profile of NCBC software
+* Improving the Internet profile of the NCBC program: Maintaining http://www.ncbcs.org/ (thanks to i2b2 for continued support of this), ensuring that all affilitated institutions (subcontracts, DBPs, collaborating R01/R21s) link to this site.  http://www.biositemaps.org/ continuing the maintenance of this and using it to maximize the Internet profile of NCBC software
 * Establishing common format for reporting (web hits, usage of software, training).  This item arose out of other discussions between participants.