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Preprint Journal Club

We are excited to launch our new preprint journal club platform http://preprintjc.org!

Why Preprint Journal Clubs?

Preprint journal clubs are a great way to keep abreast of cutting edge research in your field, and also provide feedback at a stage when it can still be used to improve the manuscript.  In other words:

“For authors, one of the most exciting potential benefits of preprints is the ability to attract early feedback from broad and diverse sources during the preparation of a scientific manuscript. Preprint journal clubs can provide this input – and a more meaningful review experience for their own members as well.”

–  Jessica Polka, http://asapbio.org/preprint-journal-clubs

For more information on the benefits of starting a preprint journal club, along with information and advice on running a journal club. see the ASAPbio Preprint Journal Club page  https://github.com/SamanthaHindle/preprint_JournalClub organised by Daniela Saderi and Samantha Hindle.

How does preprintjc.org support preprint journal clubs?

PreprintJC provides a platform for writing and sharing journal club review of preprints. In particular it facilitates:

  1. creating an online presence for your preprint journal club and listing journal club members;
  2. getting notifications of the latest preprints in your area of research, using our preprint theme pages:  http://preprintjc.org/themes;
  3. collaboratively bookmarking preprints of interest (bookmarks are shared by all members of a journal club);
  4. posting the review comments to the authors;
  5. posting comments publicly (either immediately or after authors have written a response);
  6. authors  posting their response to the review (which is displayed together with the review);
  7. keeping a record of all journal club reviews, e.g. http://preprintjc.org/journalclub/50046nn11678

 

How does it differ from Academic Karma?

PreprintJC.org is built on the same platform as Academic Karma.  Essentially preprintjc.org provides extra functionality to help facilitate journal club preprint peer review, rather than just single-person peer review.

 

Open science agreements between reviewers and authors

For #OAWeek16 we are launching open science agreements.  These are agreements between author and reviewer which are agreed before the reviewer accepts a review invitation from a journal.  We describe why we think open science agreements are needed here.  The rest of this blog is devoted to showing how open science agreements work in practice.
An invited reviewer visits http://academickarma.org/reviewagreement,  where they will find the following form.

screenshot-from-2016-10-26-131910

Why do we need open-science agreements between authors and reviewers

If you are committed to open science, there are fairly limited options for reviewing papers. Basically your only option is to review for journals which support and enforce open science principles. You are then trusting the journal  to make sure the author makes their data and code available, and also publishes the article open access.   Moreover, you are forced to decline to review interesting papers because they are not submitted to a limited number of journals supporting open science, or because the authors couldn’t afford the article processing charge and submitted to a closed-access journal.   This approach provides no feedback mechanisms to the authors of these papers that you would have been happy to review their paper had they committed to making their article, code and data openly accessible to the community.   It provides no incentive to authors to be more open.

We wanted to create an alternative, and this is where the idea of open-science agreements came from.    When you are invited to review a paper, you can visit http://academickarma.org/reviewagreement  to specify (anonymously) what you expect from the authors in terms of openness before you agree to review their paper.   You also specify how open you plan to make your review, and how long you expect it will take you to complete the review.   Rather than asking the authors to pay to publish open-access, the reviewer can ask that both the submitted and revised manuscripts are uploaded to a preprint server.   The authors can suggest modifications and explain if they are  unable to satisfy all of the reviewers expectations.  If an agreement is reached , then the reviewer can review the paper with the knowledge that their free labour is supporting resources (code, data, manuscript)  which can be re-used by everyone.

More information on how open science agreements work is provided here.

Reviewer-author contracts as a way to encourage openness in scientific publishing

In preparation for open access week, we are asking for feedback on our new initiative: Reviewer-Author contracts.

Background:

Academics review manuscripts for free  in order for publishing companies to make billions by charging readers to the access the work.   We think that a viable alternative is for scientists to only agree to review manuscripts which are first deposited in preprint servers, and to make the content of their review openly available alongside the preprint.    Reviewer agreements are a way to give the reviewer a bit more influence over the openness (open access, open code, open data)  of papers they choose to review, or at least a way for them to chose to only review papers which are following open practices.

How does it work:

1. Reviewer receives an invitation from a journal to review a paper.
2. Invited reviewer fills in the form at http://academickarma.org/reviewagreement, specifying their conditions for agreeing to review the paper.
3. Academic Karma sends an email to the paper author informing them of the conditions requested by the anonymous invited reviewer.
4. The author can either agree, decline, or modify the agreement.
5. If the agreement is modified, an email sent to the invited reviewer, who can either agree, decline, or modify the agreement
6.  3-5 repeated until an agreement reached, or either invited reviewer or author declines.
7. Once an agreement is reached, the  reviewer agrees with the journal to review the paper.
8. The author posts the preprint.
9. The reviewer reviews posts as a comment on Biorxiv preprint page, or if they want to remain anonymous, they  post the review on the Academic Karma review page and we post their comment for them (possibly  after a specified ’embargo’ to give the authors a chance to respond first).
10. The review is sent to the journal editor.
11. The author modifies the paper, re-uploads to a preprint server, and posts their response to the review

What is currently included in the review agreement:

1. Option to ask author to post preprint.
2. Option to ask author to agree to post a revised preprint.
3. Option to ask author to make data openly available.
4. Option to ask author to make source code openly available.

So that the expectations are not just on the author’s side, the reviewer can also choose to  commit to

1. The maximum time they will take for the review.
2. Whether they will agree to review a revised manuscript.
3. Whether they would be willing for their review to be transferred to another journal.
4.  How long of an embargo period before the content of their review is posted.

These ‘contracts’ are not binding in any legal sense of course.  However, a permanent record is kept so that both reviewer and author can refer to what they agreed to.
We welcome any feedback on what extra conditions we might want to include, as well as what extra optional commitments reviewers might like to make.

Scientists who open-review preprints

Peer review is controlled by publishers who generate billions in profits from free labour. What are your options if you do not want to provide free labour to be exploited by publishers, but still  want to contribute to peer review?

  1. Demand payment for peer review either to yourself, or for your department, or perhaps a contribution to a worthy cause
  2. Refuse to review for certain publishers
  3. Open review preprints

The problem with 1. is that publishers will pass that cost onto authors. A good example of Option 2 is The Cost of Knowledge boycott of Elsevier.

What about option 3?

The idea is that you only agree to review manuscripts if they are also posted as preprints, and that you publish your reviews openly online and send the link to the journal editor.  The authors can respond to your reviews openly, independently of the review process in any particular journal. The journal can still use your reviews of course, but then again so can anyone else.  Instead of doing free work for a publisher, you have instead contributed a common good from which everyone can benefit .

There is already a  group of pioneers in this space who are already posting open preprint peer review.  These scientists have between them written 61 open reviews of 51 preprints.  Undoubtedly there are many more examples (e.g. in blog posts) which have not collected here – please point us to these so that we can index them.

Not everyone is comfortable posting non-anonymous open peer review. We have created a platform where you can post content-open preprint peer review anonymously or non-anonymously. You can review any arXiv, bioRxiv, PeerJ, SSRN preprint, or even papers deposited in several institutional repositories.   If you are worried your review is overly critical and might be damaging to the authors, you can also set an ’embargo’ period to give the authors a chance to respond before the review is made open.

So here’s to those scientists who are showing us that there is a way to contribute to peer review without providing free labour to be exploited by publishers.

 

Prize for most endorsed review of #SMBE16 preprint

One of the goals of Academic Karma is to separate peer-review from publication in a particular journal.  One of the most promising ways of doing this is by the community shifting to content-open review of preprints.

In order to try to encourage this, we are putting up a $200USD prize for the most endorsed review of a preprint presented at SMBE16.

Here is a primer on how to use Academic Karma to do preprint peer review, and how to endorse preprint reviews.  Here  is a list of preprints presented at SMBE16.

The competition will run until the end of July.

Reviewing conference preprints.

Recently we tweeted the reasons for peer-reviewing but not for journals:

Its important to clarify what we mean by ‘for’ here:  we use it to mean as the primary purpose of the review. So by all means share a content-open preprint with a journal considering publishing the article.  Also, by content-open we mean making the content of the review open, but potentially choosing to remain anonymous.  Junior researchers  justifiably worry about implications of non-anonymously criticising senior researchers in their field.

One way to peer-review, but not primarily ‘for’ journals is to review a preprint which was presented at a conference you attend.  The advantages are that you get the chance to hear the author explain the work in person, and you can also ask them to clarify anything which was unclear in the preprint.

In order to make this easier, we have implemented a feature which lists preprints presented at selected conferences.  If you would like this feature enabled for an upcoming conference, you can register it here  http://academickarma.org/conferences, and let us know so we can help you curate the list of preprints.

One great example of this is the Society for Molecular Biology and Evolution conference (SMBE16):  http://academickarma.org/conference/SMBE16.

In order to try to encourage more ‘conference preprint’ peer-review, we are going to award $200USD to the most endorsed review of a preprint presented at SMBE16.  The rest of this post is a primer on how to use Academic Karma to review a SMBE16 preprint.  In order to review a preprint you dont need to register specifically for Academic Karma, but you do need an ORCID identifier (http://orcid.org).

Step 1:  Choose a preprint to review here:  http://academickarma.org/conference/SMBE16.

Step 2:   Click on the ‘Review’ link, which takes you to the review page for that particular paper. For illustrative purposes, we are going to do a review of : A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes.

Step 3:  On the review page, click on the ‘Review this paper’ link

reviewpage

Step 4: This takes you to a  login-page for logging into Academic Karma via your ORCID.  Once you have logged in you will be automatically redirected to the review page.

 

orcid

Step 5:  Write and submit the review.  You can specify who contributed to the review, whether you would like the comments sent via email directly to the author, if you would like to have the reviewed cc’d (e.g. to an editor), if you would like to sign the review, and an ’embargo period’ before the comments become publicly visible (allowing the authors to respond to the review before it goes live).

submit.png

Step 6: Thats it!    Maybe tweet the review if you would like and ask people if they would like to endorse it.

endorse

To endorse a review, just click on the endorse button (you need to be logged in, but its easy to log in using your ORCID or twitter credentials.

 

All completed reviews are listed alongside the preprints here:  http://academickarma.org/conference/SMBE16.