4D Nucleome Network Wiki

Notes drafted by Kathia Zaleta

02-13-2017 4DN POLICY MINUTES

Next meeting March 13th, 2017

\ AGENDA: - Bioarchive submissions - Publication release policy (Talk to: Bill Noble, Andy) \

1.- Bioarchive submissions

\ * Recently Dr. Gilbert tried to post a manuscript in BioRxiv and got rejected. Changes in BioRxiv policy states that they do not longer accept protocol/methods type manuscripts. * Dr. Nils Gehlenborg emailed to BioRxiv to understand the current policy and got a lot of responses. He summarized that although BioRxiv major preference is for publication biology and some 4DN manuscripts can still be posted, it won’t work entirely for the 4D Nucleome, thus is important to have an alternative. \

• Dr. Leonid has suggested to create our own 4DN nucleome protocols and make them available to a broader scientific community. The advantage is that the 4DN will have a collection of all protocols and techniques developed by the 4D nucleome umbrella. The downside is that is going to be only internal, but still make it public and for permanent search by using libraries services. For example, Harvard and MIT libraries do this.
• Discuss with Dr. Sheng (OH) to create the 4DN nucleome protocols.
• NIH (Judy Mietz) should initiate talks with Cold Spring Harbor (CSH) BioRxiv (Get the info of executive director of CSH press to start the talks)
• Nils has proposed to ask CSH BioRxiv to create a 4DN channel. For example, BioRxiv have a channel mechanisms to collect manuscript related to conferences, a channel for biology genome, etc..
• OH could link to our 4DN channel.

\ 2.- Publication/data release policy Questions: What is production data? What is technology development data? \

• Currently we don’t have any data type that is considered production data type because we don’t have established QC protocols.
• Two criteria for data type to be production data to be considered: 1) Create a metadata model to describe data and submit to DCIC & 2) Create QC pipeline to be applied to the data for quality.
• Ask Imaging WG \__to join the policy WG to establish standards.
• The policy summary is provide data, label as QC (QC happens in parallel post-submission) and make data available.
• Dr. Nils has proposed to create a minimal data model that describe, what cell lines were used, what treatments, technology, and protocols. This minimal description that DCIC can use. A potential concern is create a big policy that nobody is going to use.
• Dr. Leonid has suggested to Implement curation instead of QC.
• The idea is to make data available rapidly as possible with minimum data that can be applied to all types of data. If QC is skipped, then the data will be flagged.
• Question: What we are going to do with data that is not going be publicly released? (need to be discussed)
• During NOFIC meeting there was a discussion about when data should be public and release. NOFIC decided that this will be up to the investigator.
• Discuss with NOFIC about release policy during their meeting on March 7th, 2017.
• Is necessary to have release deadlines during the year (3 deadlines)
• NOFIC have a discussion on policy release, but didn’t considered QC, label, etc Judy Mietz suggested to present policy release during steering committee meeting and NOFIC meeting.