chem-bla-ics: May 2021

new: "A strategy towards the generation of testable adverse outcome pathways for nanomaterials"

Our BiGCaT research group studies the systems underlying biology. Here, I focus my research on the chemistry bits, and contribute with my knowledge around cheminformatics, data analysis, data representation, and software development. Marvin Martens is bridging molecular pathways (think WikiPathways, doi:10.1093/nar/gkaa1024) with Adverse Outcome Pathways (AOPs), see this paper and this preprint. He is dissemination his OpenRiskNet and EU-ToxRisk research to the nano projects, such as RiskGONE.

Now, our RiskGONE partners in Leuven, Dr Sivakumar Murugadoss and Prof.

May

EU Trials Tracker about Maastricht University

Yesterday I found in my Feedly a post in the Open Access Tracking Project feed about another tracker, the EU Trials Tracker. Reminders help us improve things. Maturity indicators help us point how we can improve things (not should). It's called formative assessment. Ranking, on the other hand, tend to be quite judgmental, which I find not so useful. When the ranking is used to make, for example, tenure or funding decisions, that's where wrong things happen.

May

coalibry.org 0.0.5 peer reviewed

Peer review is important aspect of the scholarly discourse. Honestly, right now, I'm too tied up in project work to do much peer review and the sparse time I have, should go into my editor-in-chief role. Already back to around new year, I intended to review coalibry.org but I just could not get around to it. I intended the review other websites even longer ago. But since peer review is not recognized and rewarded as an academic activity, it basically comes down to weekends. So, here goes.

May

Maastricht University elections: the university council, and The Party of the Academic Staff

Fourth post in the series about the Open Science questions with respect to the upcoming Maastricht University elections gives the answers I received for The Party of the Academic Staff, candidate for the University Council WP. With their permission to quote them, please find here their detailed answers to my questions.

May

Maastricht University elections: the university council, and LEAD

Third post in the series about the Open Science questions with respect to the upcoming Maastricht University elections gives the answers I received for the Leadership for Equitable Academic Democracy (LEAD) party, candidate for the University Council WP. With their permission to quote them, please find here their detailed answers to my questions.

May

Maastricht University elections: open science in the faculty council

So, yesterday I started blogging about the upcoming Maastricht University elections. I can vote for the University Council WP and the Faculty Council WP FHML. I assume that the "WP" is short for the Dutch scientific employees ("wetenschappelijk personeel"). FHML is the short for Faculty of Health, Medicine and Life Sciences, where I have my contract (I do work at other faculties too).

May

Maastricht University elections: positions about Open Science

University elections will take place soon and we have received some initial information about what I can vote for. Because it was not immediately obvious to me where they stand an (the issues around) Open Science, I send out emails for candidate parties with a few questions. I will be replying to this blog post with answers I received.

May

new: "A resource to explore the discovery of rare diseases and their causative genes"

The growing open access to literature greatly reduces the cost of making overviews of history of science. Freddie Ehrhart looked into the history of the discovery of monogenic rare diseases, with a particular focus on the identification of genes involved in the cause of the disease (doi:10.1038/s41597-021-00905-y):

We assembled a collection of 4166 rare monogenic diseases and linked them to 3163 causative genes, annotated with OMIM and Ensembl identifiers and HGNC symbols.