4D Nucleome Network Wiki

4DN Publications Committee

Feb 08 2016

Meeting Notes

Chair: Nils Gehlenborg

Attendees: Huimin Zhao, Larry Garace, Leonid Mirny, Shankar Subramaniam, Timothee Lionet, Olivier Blondel, Chuck Murry (notes)

Absent: Iddil Bekirov, Stephanie Alexander

1.\Frequency of meetings. Requests coming in for manuscript submissions to DCIC creates some urgency for our business. Encode policy to serve as a basis for our policy in three areas: data release, publications, software. * a.\Our next meeting will be March 14

• b.\Shoot for something to present to the steering committee in late March 2.\Tracking manuscripts to prevent conflicts and ID synergies. Nils has a draft policy document. Needs to be easy to upload, modify, track progress. Put abstract in initially, later full manuscript, update as it goes through publication. Options:

• a.\Wiki—Contact OH if you do not have access. * \i. Nils ran us through the process of uploading a manuscript. Took about 5 min to fill in basic fields. Interested parties can subscribe to updates. File formats pdf. Searchable, keywords recommended. There is a field for comments on the abstract
  • \ii. When should something be uploaded? General agreement on time of manuscript submission. * \iii. What should be mandatory: Submitting author, title and abstract, at the time of manuscript submission. Other information is optional.
• b.\Shared Google document—spreadsheet; not wieldy. * c.\GitHub—software for version control. Requires individual subscriptions. Deemed too complex.
• d.\Decision to go with Wiki * e.\Means of enforcement? Will only be as good as people’s desire to participate, but not a high level of enthusiasm for formal sanctions beyond peer pressure.

3.\Data policy. Had decided at last meeting to start with Encode’s policy and modify as needed. * a.\Data should be released to consortium no later than when the manuscript is submitted. Will be released via DCIC.

• \i. Submission earlier is OK and encouraged. * \ii. How do we protect this from being used undesirably, e.g. second party publishing before the first party?
• b.\What data should be released? Omics yes. Discussion re imaging data. Decided that Nils will consult the other two working groups. * c.\Shankar raised issue of requirements for Common Fund program data release requirements. Latest time may be acceptance of first manuscript including data. General agreement that we can set earlier submission times but not go later.
• d.\Software and source code should released for noncommercial use as well. Institutions may vary in how they handle commercial uses. To be dealt with at a later time. 4.\Nils will work with Leonid to create a list of key points regarding data release. When should data be released and to whom? This will be sent around for email discussion.