Synthetic Daisies: 10.20

October 20, 2020

ASAPBio Session on the "Past, Present, and Future of Preprints"

For Open Access Week 2020, Synthetic Daisies will feature an exciting panel discussion on preprints. On Monday (19th), I was part of a panel called "Past, Present, and Future of Preprints", hosted by ASAPBio. I live tweeted the event from the Orthogonal Research and Education Lab Twitter account. If you were not able to attend in person, the recording is on YouTube! The session started with a short introduction from each of our participants: Antonis Rokas, Soumya Swaminathan, Richard Sever, Ross Mounce, and Anjana Badrinarayan.

Yamini Ravichandran and Marco Fumasoni started us off with a short introductory presentation, followed by an introduction by each of our panelists. This part of the session culminated with Marco posing an initial question to the panel.

It turns out that there are many contributing factors to preprint adoption. Some of them involve legacy patterns from manuscript submissions and publications. But preprints also democratizes access to both the production and consumption of scientific literature. It turns out that cultural traditions (within fields and countries), researcher agency, and community incentives are also quite important.

The theme of research culture came up time and time again. But research culture is not only a motivating factor; pro-preprint behaviors can lead to other virtuous practices. For example, Ross Mounce suggests that preprints can encourage a culture of versioning, where different versions of a paper are viewed as important steps in the research process rather than simply being erratum.

There was also a discussion of the role traditional journals play in the research dissemination process. One future direction of preprint culture is to decouple papers from journals. Towards the end of our session, we heard a choice quote from Antonis Rokas and the Rokas Lab.

This combines nicely with observations earlier in the session regarding citation metrics: with the movement towards iteratively-developed preprints with multiple supporting components (open data sets, supplemental figures and notes), there will be a need to distinguish article quality from journal quality. Altmetrics are one path forward, but a more robust system is needed.

Thanks to everyone for participating! Thanks also go to Sarah Stryeck, Jessica Polka, and of course Iratxe Puebla for being a great community manager! Happy Open Access Week!

UPDATE (11/3): A recording of the session is now on YouTube!

October 14, 2020

Hacktoberfest now live!

Welcome to Hacktoberfest! Check out our DevoLearn repositories and our DevoLearn AI resources. Contribute from now until the end of October. Make five commits during the course of October, and Github [1] has something for you!

Want to participate in Hacktoberfest @ DevoWorm? Look at our issue board for Group Meetings, or look at the contribution guidelines for DevoLearn and contribute a Data Science demo.

Select issues on the Group Meetings issue board (DevoWorm) and the Community Board for DevoLearn are also marked with the "Hacktoberfest" label. Once you decide where to contribute, issue a pull request or communicate your interest as a comment in the issue you want to address!

Thanks to Mauyukh Deb and Ujjwal Singh for their administration efforts, and Github users Abtaha, Jainal09, RaviKarri, RudRajit1729, Joel-Hanson, shreyraj2002, Malvi-M, krishnakatyal, and jesparent for their commits so far!

[1] Github offers a T-shirt as incentive for contributing. Offer only applies to labeled repositories (most of the DevoLearn repositories are eligible).

October 8, 2020

Multidimensional Chess Convoluted to a Pretty Picture

At last Monday's DevoWorm Group meeting, I gave a short lecture on ways to interpret multidimensional data using PCA, tSNE, and UMAP. Here are the slides (below) and the YouTube link. The focus here is on Developmental Molecular Biology, but are generally useful, particularly for comparing methods. Here are the slides with a bonus from Leland McInnes, one of the originators of the UMAP technique!