|
|
Line 10: |
Line 10: |
| = 2106 meetings= | | = 2106 meetings= |
| [[2016]] | | [[2016]] |
− |
| |
− | =December 8 2016=
| |
− |
| |
− | ==Agenda and minutes==
| |
− | * Grant draft complete. Briefly discuss next steps:
| |
− | **Paul will take off the doc on saturday morning Dec 9th
| |
− | * LoS: who is missing and re-request plan
| |
− | **received from: ZFIN, Xenbase, RGD, Nemametrix, WormBoard, SGD
| |
− | **responded but did not provide the letter yet: Flybase, MGI, GSA, Transgeneome
| |
− | **did not respond: BioCADDIE
| |
− | ** LoS from Todd- needed?: not needed will have biosketch
| |
− | * Biosketches: need or not and for whom: prepare for all
| |
− | * Anything missing Karen and I can work on?:
| |
− | **figure 2 rearrange, make smaller, bold text in figures
| |
− | **representative example of the data model- cannot put hyperlink but url is fine.
| |
− | **Add link of the ina-1 micro pub
| |
− | **in the future we can use the platform for descriptions such as concise descriptions, pathway summaries: could be a micro publication with subheading ‘summary’ or could be a microreview
| |
− | ** put in numbers of expected micropubs we will receive
| |
− | this will help AGR -think about how to put that in
| |
− | *Arnold Foundation
| |
− | **deadline for Letter of Interest Dec 15
| |
− | **modify the current LOI and submit to Coko for review by dec 12
| |
− |
| |
− | =November 10 2016=
| |
− | Participants: Paul, Tim, Karen, Daniela
| |
− |
| |
− | ==Agenda and Minutes==
| |
− | * CoKo meeting report and Arnold's call
| |
− | ** 12 people working for Coko currently
| |
− | ** excitement on both sides for the micropub project
| |
− | ** ideas on submissions, give many options to authors: use structured form, upload a word doc, etc..
| |
− | ** generate a submission form that on half screen has fields to be filled and on the other half displays the article being compiled -> attractive for authors
| |
− | ** will be listed as contractors on the grant if we decide to put them in (U1 and Arnold)
| |
− | ** Arnold call seems to be fitting very well our scope
| |
− | ** they suggested coko and us will submit 2 separate grants to Arnold, citing each other resource as needed to carry out the project
| |
− | ** they do not have journal hosting
| |
− |
| |
− | * U1 grant
| |
− | ** sent LOI to PO
| |
− | ** write a draft by Dec 1st
| |
− |
| |
− | * IWM Workshop
| |
− | who should participate?
| |
− |
| |
− | ** GSA-> G3? Tracey?
| |
− | ** BioRxiv? Marty? Does Marty have to commit before we send out the proposal? If so, can PWS contact him?
| |
− | ** Micropubs (Daniela & Karen), shall we have someone from Nemametrix that will talk to give a user's perspective
| |
− | ** someone from coko foundation? Adam Hyde, the Coko co-founder we met, could be another potential speaker. see recent presentations: http://www.adamhyde.net/projects/
| |
− |
| |
− | =October 21 2016=
| |
− |
| |
− | Participants: Karen, Tim, Daniela
| |
− |
| |
− | 1) Replica experiments:
| |
− | -the trehalose paper was sent back because it was repeating published results -> how do we deal with it?.
| |
− | We decided to allow submission of replica experiment as long as is stated.
| |
− | At the moment of submission authors will have to tag the submission:
| |
− |
| |
− | <pre>
| |
− | Section headings
| |
− | New findings
| |
− | Methods & reagents
| |
− | Replication – successful
| |
− | Replication – unsuccessful
| |
− | Negative results
| |
− | </pre>
| |
− |
| |
− | We let the author propose the tag but leave it open to the reviewer to disagree.
| |
− |
| |
− | Shall we put a limit for submission of replica experiments? -> Yes.
| |
− | How many max? 5?
| |
− | We don’t want to have people exploiting the system and send published results over and over
| |
− |
| |
− | 2) Disclaimer: Make sure that we have a disclaimer, e.g.:
| |
− | 'by publishing i agree to make available the reagents to the community'
| |
− |
| |
− | 3) Add availability of reagents on the file, e.g. N2: CGC
| |
− |
| |
− | 4) Shall we post reviewers comments online? -> topic on the table for future discussion
| |
− |
| |
− | 5) Daniela will contact also Highwire and e-bench press to see what it would entail to work with them
| |
− |
| |
− | =October 12 2016=
| |
− |
| |
− | Participants: Todd, Karen, Paul, Tim, Daniela
| |
− |
| |
− | ==Agenda==
| |
− |
| |
− | 1) Reviewers suggestions and policy (1 vs 2 reviewers) for Nemametrix submissions.
| |
− |
| |
− | * We want to upload 4 nemametrix micropubs by the October 26th deadline
| |
− | * Need to send out to reviewers ASAP
| |
− | * To whom and how many?
| |
− |
| |
− | 2) Collaboration with the Coko foundation. [https://docs.google.com/document/d/1ioqHHxfDnDY6YioyIIrAPFKijrcZIePnZIra1YqQhSw/edit]
| |
− |
| |
− | * They are happy to support us and are developing tools that perfectly fit with our project
| |
− | * They can write LoS or write grant together with us (Software is under MIT license) -> what do we want to do
| |
− |
| |
− | 3) Format of the micropub journal pages [https://drive.google.com/drive/u/2/folders/0B_LC59YpkJJBYXFnQWh6UG13S2s]
| |
− |
| |
− | * does the proposed format look ok?
| |
− | * this is the page we will send out for review and that will be converted in PDF if the micro is accepted
| |
− |
| |
− |
| |
− | ==Minutes==
| |
− |
| |
− | 1) Reviewers:
| |
− |
| |
− | * we will have 1 reviewer and we will leave the option to be anonymous
| |
− | * we will send the first 2 micropubs to people that are aware of the project
| |
− | * will also ask authors if they have reviewer's suggestions
| |
− | * General comment from Tim: we need to put up an advertising show at the IWM
| |
− |
| |
− | 2) Coko
| |
− |
| |
− | * ok to explore partnering with them
| |
− | * K and D will set up the whiteboard session in SF to learn more and see what the collaboration will be
| |
− | * split tasks: we do curation, they do the software -> co-grant?
| |
− |
| |
− | 3) Format of the micro pub
| |
− |
| |
− | * ok as is now, will try to have a flexible format (one that allows various amounts of narrative)
| |
− |
| |
− | =September 27 2016=
| |
− |
| |
− | Participants: Todd, Karen, Paul, Tim, Daniela
| |
− |
| |
− | ==Agenda==
| |
− |
| |
− | 1) Type of submissions
| |
− |
| |
− | * For gene expression micropublications, the submission includes:
| |
− | - reagents used to perform the experiment (transgene, construct, antibody, etc..)
| |
− |
| |
− | - the read out of the experiment, i.e. image with pattern description and curated metadata
| |
− |
| |
− | * for phenotype micropublications, Nemametrix has 2 kind of tech notes:
| |
− |
| |
− | - http://nemametrix.com/trehalose-extends-healthspan-c-elegans/
| |
− |
| |
− | - http://nemametrix.com/microfluidic-epg-recordings-diverse-nematode-species/
| |
− |
| |
− | the first one falls into the micropublication scope, the second is more like a Worm Breeder's Gazette article. Discuss.
| |
− |
| |
− |
| |
− | 2) Workflow
| |
− |
| |
− | * from Submission through the form till acceptance by a reviewer we need to track the submission and store metadata in a proper way. Are we going to:
| |
− |
| |
− | - outsource to e-journal press or similar?
| |
− |
| |
− | - develop in house? Need developer time, Who is going to do it
| |
− |
| |
− | [[File:Workflow.png|thumb|left]]
| |
− |
| |
− | [[File:Tasks.png|thumb|center]]
| |
− |
| |
− | [[File:Time.png|thumb|left]]
| |
− |
| |
− |
| |
− | <br clear="all" />
| |
− |
| |
− | 3) Editorial Board
| |
− |
| |
− | *if we start a journal we need an EIC (Paul?) and an editorial board.Who will select and contact the potential editorial board, when.
| |
− |
| |
− |
| |
− | 4) Need alternative title than 'Micropublication: biology' as colons can give problems for downstream XREF (from G3 experience)
| |
− |
| |
− |
| |
− | ==Minutes==
| |
− |
| |
− | 1) Micro vs milli
| |
− |
| |
− | * Tim suggests to have narrative-containing Micropubs more similar to a short journal article
| |
− | * Those could be millipublications as opposed to just data-driven micropublications
| |
− | * Karen and Daniela will work on different types of Tech notes from Nemametrix and on Worm Breeder's Gazette articles to model that
| |
− | * multiple micropubs can be put together to have the narrative-containing (hypothesis driven) millipub
| |
− | * micropubs in the future could be a plug in we give to journal to collect metadata.
| |
− |
| |
− | 2) Workflow. Outsourcing vs in-house
| |
− |
| |
− | * Todd: outsourcing gives us more expertise but we loose control
| |
− | * Would be good to have more than one developer involved. Not much resources at the moment
| |
− | * We will touch base with the Collaborative Knowledge Foundation (CoKo, http://coko.foundation) and see what a collaboration would entail.
| |
− | * We will continue to develop forms in-house to move on with the project
| |
− | * we will generate a database with Juancarlos that will store all data but is separate from Postgres used for WB data
| |
− |
| |
− | 3) Editorial board
| |
− | * PWS can be EIC, need to define scope and build editorial board
| |
− |
| |
− | 4) Title
| |
− | * We can call it 'Micropublication biology'
| |
− | * Daniela will check with XREF if calling it 'Micropublication-biology' with a dash -as per Tim's suggestion- will also be an possibility
| |
− |
| |
− | 5) Random
| |
− | * Tim suggesting to capture crispr reagents -> having them published as micros
| |
− |
| |
− | 6) We will have another call in 2 weeks -October 11 approx- unless we have more news from Nemametrix or there is something compelling to discuss.
| |