Find, organize and discuss papers with Journal Lab

JournalLab_LogoJournal Lab popped-up on my radar this week. In a way, Journal Lab is similar to PubPeer since it allows users to post comment on research papers and start a discussion.

But Journal Lab adds a little twist to that by also enabling users to comment on specific figures. In the case of open access journal such as PloS, the figures are displayed along with the “reactions” and comments from readers. This might help start more targeted and clearer discussions.

Comment on article and article figures.

Comment on article and article figures.

Journal Lab goes beyond post-publishing reviewing and discussion by offering a “paper collections” functionality along with a convenient alert service. Journal Lab also introduces the concept of virtual journal club. With virtual journal clubs such as “RNA and Epigenetics” or “Active on PloS”, an exciting new paper is selected every week and opened for discussion.

Build a article collection and setup alerts.

Build a article collection and setup alerts.

Journal Lab was co-founded by UCSF graduate Robert Judson and social media entrepreneur David Jay in 2011. Find a recent interview by the UCSF student news paper here.

Comment on published manuscripts with PubPeer

Logo_PubPeerThe other day, I ran into PubPeer, which allows readers to comment on publications. Here’s a description directly taken from the “about” section:

PubPeer seeks to create an online community that uses the publication of scientific results as an opening for fruitful discussion. 

  • All comments are consolidated into a centralized and searchable online database. 
  •  Authors, as well as a small group of peers working on similar topics, are automatically notified when their article is commented on.
  • Pubpeer strives to maintain a high standard of commentary by inviting first and last authors of published articles to post comments.
  • The chief goal of this project is to provide the means for scientists to work together to improve research quality, as well as to create improved transparency that will enable the community to identify and bring attention to important scientific advancements. 

PubPeer is democratizing the peer review process. This is driven by the idea that publishing research results should be open to all since publishing costs are driven down by massive digitization. However open discussions and reviews should be retained to assure good science and generate new ideas.

Shifting the peer review process from before to after publication is an ongoing effort shared by others. The idea is usually to first build a community around a collection of papers then get discussion started.  I love to concept, but feel like the system is taking its time to get adopted by the masses. Why is that? Could it be because the communities are too small? Because they are too diverse maybe? Or perhaps because such comments are not taken into account to measure research impact?

Runmycode gives a second life to your code

Logo_RunMyCodeThe web 2.0 technologies can help generate new science, but can also greatly help after publication. For example, some of you are spending months or even years coding the perfect model for your study. You will input your parameters find interesting trends, publish and move on to another project.

But then what? Don’t you feel your work is left partially untapped?

What if your work could be applied to slightly different conditions or adapted to other problems? What if users from around the globe could access that code, and run it directly online?

Runmycode does exactly that. It allows you to create a companion website for your publication. The site can host a cloud-based version of your code that users can run at will. The users input the parameter, press run and generate new data. It’s that simple!

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Runmycode is a non-profit initiative. It resulted from a collaboration between many individuals and institutions, mostly located in France. I believe that this sort of “extension” to the classic publication is exactly what science needs to be more open and better communicated. Now only if a “RunMyExperiment” website for biological research could come-up…