Content Mine: scientific literature exploration through text mining

In this episode, we interviewed Peter Murray Rust, chemist at Cambridge University. Peter is also known for his work and support related to open access and open data, among his projects is the Content Mine software chain about which we talked in this episode. The Content Mine group currently offer and maintain these open source software, but it also offers consulting services to assist individuals or groups interested in the suite of software.

Content Mine is a suite of open source software designed to mine and analyze the scientific literature. Three packages are currently offered by the Content Mine group: getpapers, ami and norma. These 3 packages should allow us to download large sets of papers about a certain subject, normalize the obtained data to better explore it and then start analyzing using basic tools such as word counts and regular expressions. We explored and discussed these packages and how they could serve a researcher. You will also learn about the history of ContentMine, its team and the opinion of publishers, such as Elsevier, regarding such practices.

Zenodo: Pioneering Open access and Open data by hosting the world's research

In this episode we interviewed Krzysztof Nowak, developer for Zenodo. We have talked about Zenodo in our 5th episode Lab Scribbles: Real-time open access science during an interview with Dr. Rachel Harding. Zenodo is a platform funded by CERN and OpenAire. Its purpose is to host experimental and research data, primarily from CERN projects but Zenodo actually welcomes all kinds of datasets, codes, presentations and documents without discrimination. Zenodo is also designed to be able to host large datasets as the maximum upload size is 50Gb, which should be enough for most projects, but if your data is larger than 50Gb, you can always contact Zenodo to have this limit extended.

Another critical service offered by Zenodo is the attribution of a DOI to any kind of file(s) uploaded on their platform. This service opens new possibilities for developers and researchers as it allows them to make any kind of information citable, thanks to the DOI, and protected by a license they choose, before even publishing in a journal paper.

During this interview with Krzysztof, we first started by exploring the history of Zenodo, how it all began, and the challenges Zenodo met during its evolution. We then talked about Zenodo today: number of users, amount of datasets, kind of datasets, most dominant fields of study, etc.
We also discussed the links between Zenodo, its values and the Open Science methodology. Finally, we finished the interview by talking about futures plans and challenges for Zenodo, and asked Krzysztof to share with us his favorite dataset from Zenodo.

Scholarly communication & open access: what researchers should know with Vincent Larivière

McGill celebrated the Open Access Week International (October 23-29 2-17) with events designed to bring awareness to newer aspects of the scholarly communication lifecycle. Vincent Larivière, Canada Research Chair in the Transformations of Scholarly Communication and associate professor of information science at the École de bibliothéconomie et des sciences de l'information (l’Université de Montréal) gave a talk entitled “Scholarly communication and open access: what researchers should know”.

The complete presentation is available here and we recommend that you take a look at the slides while listening to the first half of this episode, which is the first section of Vincent Larivière's presentation. We will discover how publishing in researcher became what it is today and an explanation of how having five big companies dominate this field affects researchers.

In the second part of this episode, we will present a short interview we had with Vincent Lariviere about an interesting event which happened here, at Université de Montreal, during the summer of 2017: the library’s university refused to renew one of the big deals it had with Taylor and Francis Group and had to go through tough negotiations with the publisher. Vinvent Lariviere was part of these negotiation and will tell us a little bit more about the role he played there.

Structural Genomics Consortium's Extreme Open Science Unit launch !

In this mini-episode, Rachel Harding (creator of the open notebook LabScribbles, discussed in episode 5) and Aled Edwards (CEO of the SGC ) discuss the launch of the SGC's Extreme Open Science Unit.

As part of the SGC's ongoing plans to push the boundaries of open science, ~15 brave early career researchers funded by various disease and research foundations and charities, will be starting to write up their science in real-time in open notebooks. Rachel and Al discuss the rationale for starting these open notebooks, their hopes for how open notebooks will help the projects as well as the early career researchers running them and invite others interested notebooking to join them.

The intro song: "Every Waking Hour" by Robin Grey.

F1000Research: An innovative publishing platform with a transparent peer review system

Today's episode is about a publisher called Faculty of 1000 or F1000. We interviewed Holly Murray to understand more about F1000 and the publishing platform F1000Research.

F1000Research has a unique peer review system in which the public can access not only the content of the submitted articles but also the discussions between authors and reviewers. For more details check out the podcast episode.

The intro song: "Every Waking Hour" by Robin Grey.