RE: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[McNeeley, Todd Alexander]

It depends, if it is CDM specific, that is still on Oracle based in KC. If it 
is i2b2 then it would be sql server. 

Todd McNeeley
Senior Software Engineer, Information Management Team Development
mcneele...@health.missouri.edu  | 573-884-3297 direct | 573-219-8341 mobile  
Tiger Institute for Health Innovation | www.tiger-institute.org
 PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL

-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Monday, November 20, 2017 10:45 AM
To: dconno...@kumc.edu; McNeeley, Todd Alexander 
<mcneele...@health.missouri.edu>; jmcc...@unmc.edu; mei...@kumc.edu; 
gkowal...@mcw.edu; kosin...@mcw.edu; danh...@regenstrief.org; 
nicholas-c-sm...@uiowa.edu
Cc: abel@nm.org; btay...@mcw.edu; bbl...@northwestern.edu; 
furmanc...@icnanotox.org; mwennb...@kumc.edu; brian-gryz...@uiowa.edu
Subject: Re: [gpc-informatics] #545: Study sample and DM sample definition for 
next-d

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  tmcneeley
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-
Changes (by dconnolly):

 * cc: gkowalski (removed)
 * cc: nsmith, bgryzlak, tmcneely (added)
 * owner:  meiliu => tmcneeley
 * priority:  minor => major


Comment:

 Todd, MU is a T-SQL site, right? Are you available to start data  extraction 
Dec 8?

 Nick, Brian, how about UIOWA?


 ref Nov 16 meeting notes in comment:39.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  minor |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-
Changes (by dconnolly):

 * cc: ngraham, bzschoche, gpc-dev@… (removed)
 * priority:  major => minor


Comment:

 Replying to [comment:32 meiliu]:
 > Bernie replied on 9/13 at 9:57AM with the following:
 > October would be good if feasible. ... We will circulate ... details on
 the data pull in the next couple of days.

 Since that didn't work out, October isn't a good bet.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by dconnolly):

 Regarding the data requested for 5 Sep (comment:23): Now that we have data
 from a critical mass of sites (UIOWA, MCW, UTSW, IU, KUMC), let's track
 the others separately:

  - MU #641
  - UNMC #642
  - UMN #643

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by jmcclay):

 JM looking into holdup at UNMC

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by meiliu):

 Bernie replied on 9/13 at 9:57AM with the following:
 "October would be good if feasible.
 We will circulate “final” (ok, nothing is every truly final, but still, no
 longer “draft”) details on the data pull in the next couple of days.
 "

 Once we receive the details, we at KUMC can prototype and present to other
 sites.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by dconnolly):

 Mei, the Sep / Oct timeframe from May 4 is at-risk due to various factors
 that I noted in comment:20.

 What seems to work for data collection exercises of this sort is for
 someone to prototype the whole process and then present it to the group.
 The only way I see us get data from all relevant sites in the Sep / Oct
 timeframe is if such a presentation can happen in the next week or two,
 and even then, with SHRINE prep for the LEC and such, it's a stretch.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by nsmith):

 UIOWA was able to submit the Table 1 results today via RedCap.

 Query used,
 NextDcodeForTable1_StudysampleAndPregnancyExclusion-2017-08-22-AF.sql​

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by dhood):

 Hello,
 IU is targeting late next week for submission of this data.  Based on
 initial discussion with data analyst it is unlikely we are going to be
 able to turn this around by 9/5.

 I will keep everyone updated on our progression.

 Dan H.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[Phillip Reeder]

I submitted the data this afternoon.  The oracle script worked, just make
sure you create all of the temp tables with
https://github.com/kumc-bmi/nextd-study-support/blob/t1subset/extraction_tm
p_ddl.sql before running the script.

Phillip


On 8/29/17, 12:52 PM, "Gpc-dev on behalf of GPC Informatics"
 wrote:

>#545: Study sample and DM sample definition for next-d
>--+-
> Reporter:  dconnolly |   Owner:  meiliu
> Type:  task  |  Status:  assigned
> Priority:  major |   Milestone:  next-d
>Component:  data-sharing  |  Resolution:
> Keywords:|  Blocked By:  546, 551, 557, 571
> Blocking:  598   |
>--+-
>
>Comment (by dconnolly):
>
> follow-up from today's call (#12):
>
>  - Mei will check with Alona to see where SQL Server version is for this
> request
>  - BG (Iowa): will check with Nick to see if they will meet deadline
>  - Alex (MCW) Working on it.
>  - Mei will follow up to see if UMN is participating
>  - Phillip (UTSW) to try it and report problems or submit
>  - DH (Indiana) will send mail regarding feasibility this week
>  - Tamara working on a GPC REDCap submission destination
>
>--
>Ticket URL:
>
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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by meiliu):

 Alona replied with the most recent version of this request she sent to
 CAPRICORN sites.
 Please see attachment.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by dconnolly):

 follow-up from today's call (#12):

  - Mei will check with Alona to see where SQL Server version is for this
 request
  - BG (Iowa): will check with Nick to see if they will meet deadline
  - Alex (MCW) Working on it.
  - Mei will follow up to see if UMN is participating
  - Phillip (UTSW) to try it and report problems or submit
  - DH (Indiana) will send mail regarding feasibility this week
  - Tamara working on a GPC REDCap submission destination

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by meiliu):

 For the 9/5 data request, since only a subset of Table 1 columns are
 required, I've trimmed the code to reduce confusion. Please see
 attachment.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:  598   |
--+-

Comment (by meiliu):

 Short notice data request for GPC sites to extract data on a subset of
 Table 1 without the 'DM onset date' column and return the results to
 Northwestern by 9/5.

 Brennan has successfully run the code for Table 1 before. Since then,
 Alona has added in a few more pregnancy code exclusions (updates to the
 code below), but for the most part nothing has changed.

 --
 Pregnancy Exclusion Code Updates:

 From Diagnosis table :
 (DX like '63[0-9]._%' or DX like '6[4-7][0-9]._%' or DX like 'V2[2-3]%' or
 DX like 'V28%') and DX_TYPE = '09') or
 ((DX like 'O%' or DX like 'A34%' or DX like 'Z3[3-4]%' or DX like 'Z36%')
 and DX_TYPE = '10')

 From Procedures table:
 PX like '7[2-5]._%' and PX_TYPE = '09') or (PX like '1%' and PX_TYPE =
 '10') or (PX like '59[0-9][0-9][0-9]' and PX_TYPE='CH')

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:|
--+-

Comment (by meiliu):

 Yes, I was aware that #544 was not technically in the critical path. We
 put it in July because it coincided with other geocoding work.
 -- Mei

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+-
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 557, 571
 Blocking:|
--+-
Changes (by dconnolly):

 * blockedby:  546, 551, 571 => 546, 551, 557, 571


Comment:

 In yesterday's KUMC planning meeting, we estimated this will complete in
 October. The critical path looks like:

   - May: test data transfer protocol (#590)
   - Jun: finish lab LOINC codes, SQL (#551)
   - Jul: integrate updated geocoding data from UMN (#544)
   - Aug: finish all changes to SQL code (#546)
   - Aug, Sep, Oct: all sites prepare, submit study sample and DM sample
 definition

 Mei, the geocoding stuff (#544) isn't technically in [/depgraph/ticket/545
 the critical path for this part of the project]. I don't know if you were
 aware of that when we put this plan together. I wasn't.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+
Changes (by dconnolly):

 * cc: afurmanchuk (removed)
 * cc: afurmanchuck (added)


Comment:

 Oops; Al'ona's trac username has an extra c.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+

Comment (by gkowalski):

 From: Bernard Black <bbl...@kellogg.northwestern.edu>
 Date: March 13, 2017 at 12:08:12 PM CDT
 To: "gpc-dev@listserv.kumc.edu" <gpc-dev@listserv.kumc.edu>, Dan Connelly
 <dconno...@kumc.edu>, "mei...@kumc.edu" <mei...@kumc.edu>,
 "jmcc...@unmc.edu" <jmcc...@unmc.edu>

 Subject: RE: [gpc-informatics] #545: Study sample and DM sample definition
 for next-d

 We at Northwestern are still developing the definitions of which variables
 to capture, and exactly how.
 Once we propose a set of definitions, we will have a better sense of
 timeline.


 Bernie

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RE: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[Bernard Black]

We at Northwestern are still developing the definitions of which variables to 
capture, and exactly how.
Once we propose a set of definitions, we will have a better sense of timeline.


Bernie

*
Bernard S. Black
Chabraja Professor, Northwestern University
Pritzker Law School and Kellogg School of Management
375 East Chicago Ave., Chicago IL 60611
bbl...@northwestern.edu
tel:  law:  312-503-2784; Kellogg 847-491-5049; cell: 847-807-9599
papers on SSRN at:  http://ssrn.com/author=16042



-Original Message-
From: GPC Informatics [mailto:d...@madmode.com] 
Sent: Monday, March 13, 2017 10:49 AM
To: Dan Connelly <dconno...@kumc.edu>; mei...@kumc.edu; jmcc...@unmc.edu
Cc: btay...@mcw.edu; ngra...@kumc.edu; bzscho...@kumc.edu; Bernard Black 
<bbl...@kellogg.northwestern.edu>; gpc-dev@listserv.kumc.edu; 
mwennb...@kumc.edu; abel@nm.org; Lindsey Lynne Cook 
<lindsey.c...@northwestern.edu>
Subject: Re: [gpc-informatics] #545: Study sample and DM sample definition for 
next-d

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+

Comment (by meiliu):

 Dan,

 Yes, I am aware of the timeline. Alona indicated in her March 8 message  that 
it would be okay if one GPC site can provide the sample definition  table by 
middle of April. I'll look into your code and try to get the  desired table 
base off of KUMC data to Alona by middle of April.

 --Mei

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<https://urldefense.proofpoint.com/v2/url?u=http-3A__informatics.gpcnetwork.org_=CwICaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=CqPxCu-EywA2wo4iO-6BFqfwPQ2roHdsnjQi7SSLgLE=vSk3uDG625n-cJWg9IV9UqBwihtENBBNorAxioC_pqc=SyAs4Nvpwf0BL-AjjRYqjah7nsY_ibzcAeZwJcbgNz0=
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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  meiliu
 Type:  task  |  Status:  assigned
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+
Changes (by dconnolly):

 * cc: Abel.Kho@…, lindsey.cook@… (added)
 * owner:  tmcmahon => meiliu


Comment:

 Mei,

 As you may have seen, Tamara let me know that [[GROUSE]] remains a higher
 priority for me. And we're still standing by for an update from MCW on
 #551. And milestone:cdm-cycle3 is a priority in the April timeframe. So as
 far as I'm aware, no GPC site is in a position to produce a sample
 definition table in the mid-April timeframe requested in Al'ona's March 8
 message.

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  task  |  Status:  new
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+

Comment (by dconnolly):

 The EDC reports we shared in #571 answer the date shifting questions among
 others.

 I just added a p.s. on date shifting in ticket:571#comment:11

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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  task  |  Status:  new
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+
Description changed by dconnolly:

Old description:

> The task is to collect these data from the 7 participating GPC sites
> (ticket:398#comment:10).
>
> For an overview of the project and our role in it, see discussion in
>   - [http://listserv.kumc.edu/pipermail/gpc-dev/2016q4/003463.html 20 Dec
> gpc-dev meeting notes]
>
> A draft of detailed SQL code is available in
> `NextDextractionCode_12.1.16.sql​` attached to #539.
>
> Note the use of SFTP site provided by Northwestern rather than GPC REDCap
> (#542).

New description:

 The task is to collect these data from the 7 participating GPC sites
 (ticket:398#comment:10).

 For an overview of the project and our role in it, see discussion in
   - [http://listserv.kumc.edu/pipermail/gpc-dev/2016q4/003463.html 20 Dec
 gpc-dev meeting notes]

 A draft of detailed SQL code is evolving in https://github.com/dckc/nextd-
 study-support
 (based on `NextDextractionCode_12.1.16.sql​` attached to #539).

 Note the use of SFTP site provided by Northwestern rather than GPC REDCap
 (#542).

--

--
Ticket URL: 

gpc-informatics 
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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  task  |  Status:  new
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551, 571
 Blocking:|
--+
Description changed by dconnolly:

Old description:

> A draft of detailed SQL code is available in
> `NextDextractionCode_12.1.16.sql​` attached to #539.
>
> The task is to collect these data from the 7 participating GPC sites
> (ticket:398#comment:10).
>
> Note the use of SFTP site provided by Northwestern rather than GPC REDCap
> (#542).

New description:

 The task is to collect these data from the 7 participating GPC sites
 (ticket:398#comment:10).

 For an overview of the project and our role in it, see discussion in
   - [http://listserv.kumc.edu/pipermail/gpc-dev/2016q4/003463.html 20 Dec
 gpc-dev meeting notes]

 A draft of detailed SQL code is available in
 `NextDextractionCode_12.1.16.sql​` attached to #539.

 Note the use of SFTP site provided by Northwestern rather than GPC REDCap
 (#542).

--

--
Ticket URL: 

gpc-informatics 
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Re: [gpc-informatics] #545: Study sample and DM sample definition for next-d

[GPC Informatics]

#545: Study sample and DM sample definition for next-d
--+
 Reporter:  dconnolly |   Owner:  dconnolly
 Type:  task  |  Status:  new
 Priority:  major |   Milestone:  next-d
Component:  data-sharing  |  Resolution:
 Keywords:|  Blocked By:  546, 551
 Blocking:|
--+
Changes (by dconnolly):

 * cc: gpc-dev@… (added)


Comment:

 An updated timeline from Charon estimates:
   - 24 Feb: finalized study code version distributed to CAP/GPC
   - 3 Mar: final date for CAP/GPC sites to package and submit data to NU
 for analysis

 That's a 1-week turn-around time. To manage that, it'll be important to
 keep code available as it evolves so that sites can practice in advance. I
 have started to use github for this (ticket:546#comment:9) and Al'ona
 writes 3 Jan that she plans to do likewise.

--
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