Difference between revisions of "Calls"

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*Number of visitors still increased- 241 unique/week, 682 page views
*Number of visitors still increased- 241 unique/week, 682 page views
=May 30 2017=
===ZFIN participation===
* ZFIN community interested in micropublications. Karen, Tim, and Daniela had a call with him last Thursday (minutes here https://docs.google.com/document/d/1ujSN6p_-k-lh7WTRMgWq8A_hGqbk0dAv5kN9hDAIdGk/edit).
After the meeting Doug started working on a phenotype submission form draft:
‘I'm currently working with Leyla Ruzcka on a draft submission form for phenotype data.  My current best estimate on a time line for that is that we would start talking with developers here about it some time around the end of July, and if it went well, would be thinking about implementing the form in the August/September time frame.  Let me know if that time line causes problems on your end...we can always push it out further if desired...probably couldn't move it up sooner though.’
===Copyright issues===
* Doug asking:
‘Have you guys thought about copyright issues at all WRT micropublication?  For example the disclaimer I see on some of your submission forms could say something like "I understand that this submission will go through a peer review process and upon passing peer review will be added to the ZFIN database in an open acceess format.  Copyright remains with the data submitter. Where DOES copyright remain, and are micropublications open access?’
* Contacted Jane Mendel to see if WormBook had to get formal licensing from Creative Commons
===Publisher issue===
*Shall we start contacting EZID and ask about using ‘micropublication: biology’ as publisher?
===Website stats===
*Number of visitors still increased- 169 unique/week, 634 page views
===Knudra submission===
* Any news from the reviewer? Shall we send out to another one?
* Paul contacted him-waiting for reply
* Micropublication: biology button on the WB homepage -> should be up? on which release? WS259?
* Todd -> Twitter account? need changes in DNS records?
===IWM booklet===
* Karen and Daniela will meet Nemametrix designer tomorrow
* Started to work on a phenotype submission form
===Corrections post publications===
* how shall we deal with them? If it’s a simple typo shall we just manually edit it?
* if it’s a major change: tim’s suggestion:
“there should be some note on the article indicating that it it a corrected version, with the data of the new version, below the published online date.”
* example of journal's policies:
===ZFIN participation===
* the sooner they can start the better
===Copyright issues===
* will wait to hear from Jane and talk again with Doug about it
* Ok to keep Doug's disclaimer suggestions and also keep our current disclaimer
===Publisher issue===
* We will contact EZID about having Micropublication:biology as publisher (Daniela will do)
* Joan Starr replied the approach is fine, can put Micropublication: biology
===Website stats===
* Number of visitors still increased- 169 unique/week, 634 page views
* We want to tell users that we are at the 'pre-beta' (alpha) stage, meaning at the very beginning
===Knudra submission===
* Tim will review
* Tim: is Knudra asking money for reagents? are we acting as advertisers?
* Karen will find out if they deposit data at the CGC or of they will distribute it for cost
* Is an allele-sequence enough to be a micropublication?
* Is an antibody enough to be a micropublication?
** We need to discuss this further when Paul/Todd are around
** An antibody should be micropublished with an expression pattern
** A mutant should have a phenotype attached (or a phenotype NOT observed attached)
** Tim: we should have a phenotype AND allele together. What is the utility of having just the reagent? there should be useful information behind it.
* Paul contacted him-waiting for reply
* Micropublication: biology button on the WB homepage -> should be up? on which release? WS259?
* Todd -> Twitter account? need changes in DNS records?
* Started to work on a phenotype submission form. Juancarlos could also help set up a database if we design pages with html editors. We could have micropublication tables and the database will read into those (good for the future, and for large scale submissions).
===Corrections post publications===
* corrections-> if it’s just a typo we could change it ourselves -> not scalable if we get large volumes
* change in substance -> Have an Errata corrige -> Separate DOI? Yes, Errata get different DOIs and different PMIDs
* Publish retraction -> separate DOI
===Author contributions===
* we will have Credit taxonomy implemented
=May 23 2017=
=May 23 2017=

Revision as of 17:12, 18 July 2017

July 18 2017


Progress Report

  • IWM sign-up sheets, 69 names, 8 interested in reviewing
**create a mailing list for uPub announcements
**start database(?) of interested people and possible roles - authors, reviewers

Needs discussion/decisions

  • micropubs vs data submission to WB: What to do when users only want to submit data and not micropublish? ex. Updike submissions
    • Daniela: One thought is that WormBase does not take personal communications any more- to my knowledge. So the micropub seems the only way to get these data out.
  • Coko collaboration: When should we start discussions with them?
  • Editorial board: Any more thoughts on who to have?
  • Logo: Use Nemametrix designer? ~700USD ($75/hr); Who did the AGR logo and how much was it?

June 13 2017



  • poster: final version [[1]]. Please look at it by Wednesday June 14th, will print Thursday June 15th.
  • Booklet- we sent final edits to Nick- he will leave tomorrow morning. If you have anything to bring up do it asap

To print (Daniela will do)

  • Poster
  • Banner (need to generate high res images). Banner example [[2]]. Do we need to ask a professional designer for final logo design? (after the IWM)
  • Changed: capital M in 'micropublication:biology' for banner - will change on the site
  • 15 color copies of each micropub (double sided). We have 9 micropubs.
  • Signup form for people to leave their contact info

Lanyards (Karen will do)

Workshop presentation

  • Will work on it this week and send out by Friday for review


  • We plan on giving out one 20$ amazon voucher every day (at the end of poster sessions) for people that will try out the form:
  • shall we start advertizing it on the blog this week?
  • if so, shall we add the following at the beginning of the form:

'Anything submitted from now will be entered into a drawing at the IWM for a 20$ amazon gift card. Test submissions will also be entered, check here (checkbox) if you enter only test data.'

  • We added info on the booklet on when prizes will be announced (at the end of the poster presentation)


  • they will present a poster at their booth in Budapest - we gave them ours as an example


Instructions for authors

  • Started incorporating on the site. Would a structure like [[4]] work?
  • do we need detailed guidelines like the ones [[5]]?
  • Disclaimer: 'I/we declare to the best of my/our knowledge that the experiment is reproducible, that the submission has been approved by all authors, and that the submission has been approved by the laboratory’s Principal Investigator [include the email address of the PI]. The author(s) declare no conflict of interest.'
  • Will talk to Juancarlos and see if better to pull out the PI's e-mail address from the laboratory class or if better they specify it


  • We will need to change the site from Weebly to something else (Wordpress, Open Journal System, or anything else?)
    • Better for content management (Scaling up)
    • Management of DNS records
    • We can discuss it in person at the IWM but wanted to bring it up (Todd's input immensely appreciated)

Shall we have another meeting before the IWM?

  • Daniela will fly out next Tuesday


  • Paul working with Kristen on pitch for Arnold.
  • Still waiting to hear on U01


  • have two sets of full glossy printouts of pdfs - display in binder at the table in sleeves
  • lanyard with different stickers, these will be special, not everyone gets one, community only gets them if they participate somehow - one sticker for both authors and reviewers - I micropublish
  • advertise on the blog, but do not allow raffle submissions until the meeting starts
  • will post the booklet cover
  • only print ~600-800


  • ZFIN meeting July 3-7
  • Paul will let us know what slides and info he needs, he will push Micropublication hard at the meeting. Make sure he has the booth number, raffle information, etc.
  • how do we work with other communities, we need to avoid the notion that micropublication is more than just a database curation tool. paul will clarify the message
  • Daniela will bring in Xenbase, will talk to grad advisor
  • expansion to API tools such as genomic tools like Apollo and Galaxy - perhaps a different journal Micropublication:genome analysis for example.

author instructions

  • Tim happy with Author instructions and over all structure of the page is fine
  • add request for feedback in Author acceptance letter
  • leave out detailed submission form instructions
  • good for PI to get the e-mail upon submission
  • form already has instructions for people with no laboratory designation, Tim: discuss genenames list. may need to have a micropublication specific genenames e-mail? or fix e-mail to be filtered
  • will add acknowledgement to submission form


next meeting?

no, unless there is a major disaster

  • Tim traveling starting Thursday, so won't be available for feedback
  • we will be getting feedback from WormBase

June 6 2017



  • Booklet: Wenlan needs feedback asap, prices will go up, the designer needs our input to move forward
  • Banner: should we have a banner to put on the table booth? Shall we have an extra poster instead? The banner could be a cheap paper one

Content of a micropub

  • we recently discussed (Karen, Tim, Daniela) if an engineered allele (or an antibody) could be micropublished per se or if it needs to be part of an experiment (e.g. antibody to determine protein localization for an expression pattern entry).

Publisher issue

  • As per Joan Starr reply we will change the publisher to Micropublication:biology
  • Will edit previous submissions


  • Knudra micropub online -we are just waiting for a high res picture to replace the existing one

Phenotype Submission form

  • We are working with Juancarlos on the form, might be ready next week


IWM booklet

  • keep the worm (e-mailed nick)
  • cheap banner(daniela will print)

Content of a micropub

Tim: we need to have a validation that the experiment does something biological


  • if it’s an allele that has a previously published with phenotype -> it is ok to micropublish the sequence
  • if it’s a new allele with no phenotype they have to submit the phenotype through the phenotype form.

see general discussion below:

mitani: if mitani alleles are lethal or viable it’s useful information
Karen: Knudra strains: gene replacements submission has allele and phenotype
one was the construct itself because there was a gel showing the deletion.
Paul: as long as it has content it’s fine
Tim: for knudra is a commercial entity -> advertisement
shall we set a rule academic vs non academic

2 different submission forms: one for commercials and one for academics, 
Todd: scientific standards should be the same. Distinguish from a commercial entity

Paul: same standards -> they don’t need to add more data but they have to pay. There should be a disclaimer -> paid publication
Tim: Micropublication biology does not endorse specific companies. Set a higher bar for everyone else.

"Publication in Micropublication:Biology does not imply endorsement of the products or reagents describe within."

Instruction for authors

  • we should have instruction for authors (Daniela and Karen will work on it).


  • Todd: standardize if calling it micropubs or upubs
  • look at the website and improve (Karen, Daniela, and Todd will meet this week to discuss)
  • instruction for authors ready to go before the meeting
  • mailing list (DNS records) Daniela & Todd will talk

Website stats

  • Number of visitors still increased- 241 unique/week, 682 page views

May 23 2017


  • U01 results -> when is the advisory council meeting?
  • update on submissions
    • Wang accepted
    • prahlad submission rejected by 1 reviewer, contacted another reviewer for second opinion.
    • Knudra submission sent out for review
  • booklet -> will send to nemametrix once all submissions are in for final design
    • deadline for sending for printing June 7th
  • E-life
  • IWM: poster, sign up form, glossy print outs of the micros, banner
  • Twitter account, atmicropublication.org -> todd any update?
  • Submission options:
    • The current Submit Data should be changed into Curate data (to discuss at WB group meeting)
    • Submit data should be just micropublication
  • put out new blog post once pending submissions are accepted
    • #1: e.g.: 'join the Prahlad lab, Sieburth lab, knudra and micropublish on micropublication:biology...'
    • #2: when allele-sequence form is ready: 'publish your sequencing data..'
    • #3: when allele-phenotype form is ready: 'publish your phenotype data..'



  • council has been completed.
  • Paul wrote to NIH. The NIH person in charge is on vacation.


  • Ask Prahlad to do what the reviewer suggested. we give it a chance to fix it


  • might be a little while before they get back to us, Matt B is swamped with other stuff. Karen will find out.

eLife discussion

Patterson: arnold like to put people in touch with each other. Stebbins was saying to have something big and use an existing brand and use other infrastructures.
Patterson was at plos and started currents, minipub style with no database connections.
it was also interfering with their business model (Plosone) 
Patterson: Paul would like to ask what they can do to help.
Tim: part of it is the main bread and butter is going to be the micropublication or the minipublication
Having the publisher infrastructure will help out. If micros are the main route he’s not sure we need to deal with a publisher.
Paul: I want to see everything built from the ground up. Micros first and minis built up on that. Links to database is important. bottom line is where do we get fundings. If we have no funding we need to partner with someone- some .org publisher, university libraries, commercializing it? (not ideal). 
If you build it up in pieces what parts do we build ourselves and what we give out to people.
Todd’s argument is to have a platform that everyone uses. what is todd envisioning as platform?
Todd: technical thing, how do we approach the engineering, if we build it in a such a way that other people could easily plug in into their system it would be like an API that they can integrate. We develop a development platform that other people can incorporate. 

Paul: like high wire 
todd: if the grant comes through we do it like this. if we want or need to commercialize we could go that route as well. 
Tim: in terms of clients: micropub is now just for worm, 
Paul: we want to develop the infrastructure flexible enough to plug in whatever species or data. 
todd: Elsevier would want to have our platform because it creates more engagement with the community. Encourage the collegial sharing
Tim: who would elsevier use our model 
Todd: if we are funded we make us available as a service
Tim: e-life is more compatible than Plos
Paul will talk to patterson and Kristen in 2 weeks. 
the way we go about building this out -if we have open ended design it will be beneficial
Paul: colleagues in geology and astrophysics that have the same issues and are interested
Tim: part of the design is to go out of our usual stakeholders and see that we don’t automatical exclude them 
Karen: in terms of funding: our funding is specific to the biological field
Todd: if it’s designed in an open ended fashion we could apply to other societies
Karen wants to expand the mark-up but where are the authoritative databases?
Todd: providing avenues to publish scientific observations that would never see the light of day and cross-referencing to databases.
Paul: he talked to fly persons and they are interested.
Tim: at some point we’ll face the issue of making it a sustainable operation.

Outreach and social media

  • Todd signed up for a twitter account and he generated the username micropub7n
  • will see if he can ask to have micropubs
  • todd needs to make small changes to the DNS records of the domain so we can get the list done- will get in touch with Daniela

Submit data vs curate data

  • will ask juan carlos to have a pop-up when users submit that will ask:has this information been published before? if yes will redirect to the curation form, if no will go to micropubs

May 16 2017


Arnold foundation

  • Update from Paul on Arnold's call
  • Update Coko on the call's outcome?
  • Next steps


  • Update on submissions
    • Prahlad
    • Han
    • Knudra
    • Jorgensen?

Micropub button on WormBase homepage

  • Todd can we prioritize this?

TWU visit

  • people interested in the micropub idea
  • asked if micros are visible in Google and Google Scholar


Arnold foundation

  • Paul talked to Mike Stebbins and Kristen (Coko)
  • Arnold is really excited about it, and they were trying to figure out what to do in this area. They wanted to know if it was a worm specific endeavor or a general one -> general one
  • Stebbins thought that to do it right we have to partner with a publisher to really get it going -> e.g.: e-life? mark patterson
  • Todd contrasting the idea, maybe partner with a technology company (Google?)

Micropub button on WormBase homepage

  • Will be live in the next WB release (next week or so)


May 9 2017


Arnold foundation

  • LoS for Coko
  • Update from Paul (Mike Stebbins)
  • Action plan
    • depending on IF and WHEN we will need to submit a proposal for Arnold:
- submit same proposal if U01 is turned down? will need to expand
- talk openly with Mike Stebbins and disclose that we are waiting on the NIH response and will tailor the Arnold proposal accordingly?
- if Coko gets the Arnold grant and we don’t, would they still build our infrastructure

Micropublication form updates

  • Added suggested reviewer field
  • Added title field
  • Added ISH

Potential submissions

  • Veena Prahlad (reviewer of a previous micropub) wants to submit smFISH data

Website views post blog

  • Still increase of website views


  • will send examples as soon as we get data not shown/unpublished for their journals

Micropub button on WormBase homepage

  • Todd can we prioritize this?



  • Stebbins cancelled the meeting, we'll see if we hear back

May meetings


April meetings


March Meetings


2106 meetings