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Bioclipse git experiences #2: Create patches for individual plugins/features
This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another. A second use case can be a file that must be removed (there are valid reasons for that). Because these posts are based on Bioclipse work, there will be some specific terminology, but the approach I regularly apply in other situations. -
Bioclipse git experiences #1: Strip away unwanted plugins
This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another. A second use case can be a file that must be removed (there are valid reasons for that). Because these posts are based on Bioclipse work, there will be some specific terminology, but the approach I regularly apply in other situations. -
new project: "COVID-19 Disease Maps"
Project logo by Marek Ostaszewski. CC-BY. Already started a few weeks ago, but the COVID-19 Disease Maps project now has a sketch published, outlining the ambitions: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms (doi:10.1038/s41597-020-0477-8). -
new paper: "Wikidata as a knowledge graph for the life sciences"
A figure from the article, outlining the idea of using SPARQL queries to extract data from the open knowledge base. As a reader of my blog, you know I have been doing quite some research where Wikidata has some role. I am preparing a paper on the work I have done around chemicals in Wikidata, based on what I presented at the ICCS with a poster. So, I was delighted when Andra and Andrew asked me to contribute to a paper outline the importance of Wikidata to the life sciences. The paper was published in eLife, which I’m excited about to, as they do a significant amount of publishing innovation.
