Re-organization of data sheets related to all 4DN personnel, affiliations, roles, labs, PIs, funded RFAs. Assigned to Xiaoyi, Riccardo, Kate in January 2018. New data schema and design document updated on 2/8/2018.

Video recording, production, and releasing 4DN webinars. Assigned to Xiaoyi Cao on Nov 3, 2017.

Task: get and summarize consents from webinar speakers. Report consent status by Nov 10, 2017 by writing beneath this line and sending email to oh@4dnucleome.org and szhong@ucsd.edu.

The background image for 4DN web portal header can be downloaded here:

https://drive.google.com/a/eng.ucsd.edu/file/d/0B4D9q1N_g3nCUVNjRmRRa0JfRDQ/view?usp=sharing

https://drive.google.com/file/d/0B_sCYsP4AJGwWE1CUzZmdGw1WTQ/view?usp=sharing (01/13/2017)

Access to the following document is restricted to NIH officials and OH PIs and staff.

1. OH will put together a survey to get an idea of 4DN network members attitudes about data sharing (both internally within the network, as well as with the external user community.

• OH will develop a set of proposed questions. The following is proposed on OH internal workshop on August 26th.

Data sharing survey

OH is tasked by NIH to deliver the following survey on data sharing policy.

1. What time do you feel comfortable to share your data within the 4DN consortium?

By data production

By data production and validation

By manuscript submission

By publication

2. To what extent do you feel comfortable to share the data prior to publication (multiple choice)?

Processed data

Raw data

Metadata including cell type and treatment condition

The methods and protocols on data generation together with the data

—

- OH will run these questions by Nils/Leonid

The questions were provided to Nils and Leonid on August 27, 2016.

- OH will send out the survey to the network and request their participation

- The timeline on this is: Responses should be in before the next 4DN SC meeting (September 20th).

September 9: Dr. Judy Meitz suggested that the Policy WG should be given sufficient time to prepare the survey, beyond the Sept 20th SC meeting.

2. OH and DCIC will work together to integrate the data portal with the OH portal.

• September 15, 2016: Initiated redirection from data.4dnucleome.org to DCIC's Amazon S3 data services, including ns-319.awsdns-39.com. ns-1478.awsdns-56.org. ns-2008.awsdns-59.co.uk. ns-796.awsdns-35.net. By OH staff Xiaoyi Cao, in coordination with DCIC staff: Jeremy Johnson and Burak Alver.

3. Suggested updates to the web portal (8/29/2016)

The Home Page:

·There is no easily accessible “About” section on the homepage that describes what “4D Nucleome” is or that it is a program/consortium. It might be useful to have something on the homepage that briefly describes the program (see the “Program Snapshot” on the Common Fund page for an example) AND the purpose of the portal. It should be understandable to someone outside the consortium. (9/2/2016)

·“Welcome to 4DN Portal” should read “Welcome to the 4DN Portal” (9/1/2016)

·The Data, Software, and Training links on the homepage need more description. Are these resources generated from the program or training on how to use the program resources? If not, their purpose should be stated in the description. Why would someone need to access these links? Where did these resources come from? (9/9/2016)

·The “Software” links to “Genome Interaction” and the email address listed is: “rcalandrelli at eng dot ucsd dot edu”. Might want to reformat this email address. (9/1/2016)

·The “Training – education and outreach materials” is not an accurate description for the “4DN Library” link. I suggest changing that heading to “4DN Publications” or something similar. (9/1/2016)

Note: The heading “Training” remained the same. A new field has been added to the homepage named “Publications”.

·The “Tutorials on 4DN communication tools” is unclear. Are these tools for the public to communicate with the consortium? Whom is communicating with whom? I suggest moving this link to the left side bar and/or clarifying with “For Consortium Member Only” or something along those lines. This should be done for all password protected links to avoid confusion from non-consortium members. FYI – the Youtube video that describes all of the password protected sites is viewable to the public. (9/9/2016)

The Left Side Bar:

·The “4DN Wiki” is password protected, this could also be labeled “For Consortium Member Only”. There seems to be a lot of protected links and it might be best if all of these are populated under this heading, on the left side bar. (9/2/2016)

·The “4DN Publications” link is the same as the one listed under “4DN Library”. Is there a reason for this? The same as the “Software” link, it is listed twice. I suggested either linking out to everything twice, in the same order as the homepage, or removing duplicates. (9/1/2016)

Note: the links in the homepage have been also inserted in the side bar.

·Why is the overview of the 4DN program buried in the left side bar under “Funded Projects”? The overview should be easily accessible on the homepage. (9/1/2016)

Note: the overview of the 4DN is now the first item of the left side bar.

·The External Advisors are also listed under “Funded Projects” for some reason. Also, FYI these names and emails are publically available.

Note: ESA names are still publicly available but emails have been removed from the “External Advisors” page. (9/6/2016)

Note: “Funded Projects” and “External Advisors” have been both moved under “Overview” and an “NIH 4DN Overview” entry has

been created for better organization. (9/9/2016)

Note: The overall layout of the site was revamped to provide easier navigation and cleaner UI. (9/6/2016)

4. More updates to the web portal (9/19/2016)

• Texts has been enlarged for menu and main page texts
• Navigation menu appears darker.
• Cover image now in a lighter shade; title texts and introductory texts are changed to a dark color in response to this change.
• Updating of the Software section style according to the new style of the portal.

5. Latest 4DN Publications in the web portal homepage (10/21/2016).

6. The pdf of the 4DN 2016 Program is now updated with links to all the presentations. This new version of the program replaced the old one stored at the meeting wiki page (10/26/2016).

7. The 4DN Technology Survey is live and receiving responses from 4DN PIs (10/21/2016). A summary has been provided on the Technology and data type page. (10/27/2016)

8. (Lucie) An initiative was taken to create anexhaustive list of techniques used to unravel the 3D structure of the nucleus. The list was initiated by OH and NIH members in October 2016. Protocols and Pioneer research paper were associated to the techniques when available.

As a long term approach, this list will be completed, updated and implemented by every member of the 4DN consortium.

9. Meeting Report: 2017 4DN Annual Meeting (Oct 30, 2016)

10. (Lucie) The list of genomic technologies developped in the 4DN network has been uploaded in the 4DN portal as “Protocols”.

it also included the reference paper and a short description of the technique.

The list contains unpublished techniques that will need to be updated with protocols and publication links when they are available on pubmed.

11. The 4DN Technology Survey is closed and the final results can be seen on the Technology and data type page from here (11/14/2016).

12. Email received on 11/16/16 from Dr. Chadwick with the following requests:

• Create a section on the 4D Nucleome website that is linked to the approved policies
• Approved and latest policies can be accessed on GitHub (easy to track changes and freeze released versions, no need to update any links when the policies are updated. See below:

   Publication Policy: [[https://github.com/4dn-dcic/4dn-policies/blob/master/4dn-publication-policy.md#4d-nucleome-project---publication-policy|https://github.com/4dn-dcic/4dn-policies/blob/master/4dn-publication-policy.md#4d-nucleome-project---publication-policy]]

   Software Sharing Policy: [[https://github.com/4dn-dcic/4dn-policies/blob/master/4dn-software-sharing-policy.md#4d-nucleome-project---software-sharing-policy|https://github.com/4dn-dcic/4dn-policies/blob/master/4dn-software-sharing-policy.md#4d-nucleome-project---software-sharing-policy]]

   More information about the policies (including citation information) can be found here: [[https://github.com/4dn-dcic/4dn-policies|https://github.com/4dn-dcic/4dn-policies]]

• Should be on the Public Portal
• Create a new section on the wiki side bar: Network Policies; and add put approved policies here too
• Let Dr. Chadwick know once the policies have been posted. (done 11/16/2016)

13. 4DN funded publications list and latest 4DN publications on the homepage have been updated (12/22/2016).

14. 4DN Portal Homepage revamp (1/12/2017).

15. 4DN Pre-Prints available on the Portal under the section Publications (1/20/2017).

16. 4DN Steering Committee approved protocols section in the 4DN Portal (2/21/2017).

17. 4DN Portal Homepage revamp (2/23/2017).

18. Document a feasible procedure of providing DOIs to 4DN pre-prints and other materials: Memorandum on providing DOI to 4DN pre-prints (2/23/2017)

19. Updated Webex email to oh@4dnucleome.org and also changed contact (3/1/2017)

20. Removed redundant entries (200+) in wiki sharing list to make it synchronized with 4dn-network@4dnucleome.org and other Google groups. Also added the Google accounts of 4DN members (90+) to 4dn-network@4dnucleome.org and other groups. (3/2/2017)

• The 4DN member contact list has been updated and can be accessed here (https://docs.google.com/spreadsheets/d/13gFjHcYEwYL2Xpr9-IHtJNYYnYlAQVdyXvCUeSzla6w/edit?usp=sharing);
• The 4DN-Network Group has been synchronized to the member contact list;
• 4DN Wiki access list has been reworked. Now it depends on 4DN-network Group to determine accessibility. This made the access to 4DN Wiki always synchronized to the 4DN-Network Group.

21. The 4DN network contact list is updated by 4DN PIs. OH documented quarter-by-quarter which PIs updated the 4DN network contact list.

22. All NIH 4DN listservs has been updated (4/14/2017)

• Now people outside the list can also send an email to any of the listservs. However, they will need to confirm their messages if they are not on the list.
• Confirmation mechanism has been changed so people sending message from external addresses will get an acknowledgement email.
• All 4dnucleome@gmail.com has been changed to oh@4dnucleome.org
• Mail template for post confirmation has been updated to add contact OH contact emails.

23. The name of oh@4dnucleome.org has been changed to “4DN OH”. (4/12/2017)

24. OH has registered several subdomains and approved certificates for said subdomains for DCIC: (04/03/2018)

• data.4dnucleome.org
• foursight.4dnucleome.org
• higlass.4dnucleome.org
• mastertest.4dnucleome.org
• staging.4dnucleome.org
• testportal.4dnucleome.org

25. Upgrade the 4DN wiki

• The platform of the current 4DN Wiki, the classic Google Sites, is being phased out. Currently the service is not being actively maintained by Google, which impacts the usage of 4DN Wiki to some extent.
• 4DN OH is aware of this situation and is in the process of migrating 4DN Wiki to a new platform.
• Current progress:
  • A working wiki platform has been deployed on a testing server managed by 4DN OH.
  • 4DN OH is testing the new wiki platform and migrating old wiki data to the new one.
• Migration time: 4DN OH will announce the migration time via a network-wide email announcement in February, 2019.
  • The migration time will be the time when no new updates shall be made on the current 4DN wiki. Please keep using the current 4DN wiki before this time point. All updates will be migrated to the new 4DN Wiki.
  • At the migration time, the current 4DN wiki will be taken offline to complete the final steps. When the new 4DN Wiki is online, another announcement will be made to the entire network.
  • All members shall be able to access the new 4DN wiki via the Google Account they previously use for the current 4DN Wiki.