After having kept in my laptop for a long time, I’ve pushed some notes about git and github on line. They cover the workflow I use to work on code bases, tips ‘n tricks about git/github, aligning branches and remote/local repos and more. I am often asked about many of these things, so I hope having it published will be useful.
This is an update about the AgriSchemas project (mostly), which I gave today to the ELIXIR Plant Science community. Despite we are busy with many other tasks at KnetMiner, we have done quite a deal of work with representing knowledge graphs using what I call "lightweight schemas", that is BioSchemas, schema.org, Dublin Core and the […]
Making Data Deeply FAIR through Lightweight Standards, the KnetMiner and ELIXIR CasesRead More »
This post was inspired by one of my students. As it happens, it started with a few questions in a chat, which were essentially like: since you’re a senior in this field (ie, I’m getting old, personal note…), I’d like to ask you some advice on what job is best, should I do a PhD, what are the other options (education, training, etc) to work as a bioinformatician, what about salaries, success chances, challenges, etc, etc.
After having had to delay a well-thought and comprehensive answer, I decided that maybe it was worth organising my notes on the not-so-easy topic and writing a public post, so that it could benefit everyone.
Recently, in my team, we have managed to start periodic talks/discussions on software engineering, including best practices, project management tools, code style, testing and all that jazz. If you are in a large-enough team in a full software house, probably you’re thinking: well, this kind of meetings should be pretty standard in this business. Well, […]
The Continuous Integration idea is great: people send their software code changes to a shared repository like github, and the CI reacts by building the executable product on the fly, and even using it to redeploy test servers and make latest cool features available for testing and showcasing.
In this short presentation, I show how I manage my continuous integration jobs from one script for all my projects and without (too many) dependencies on any specific CI software.
A window manager is a computer application that eases the use of multiple shell sessions at the same time.
In this post, I’ll show how you can create Maven projects that spawn command line tools. I’ll be using the great picocli library, and I’ll show how a new CLI project can be quickly generated, starting from my Maven CLI archetype.
My Maven Archetype for Java Command Line ProjectsRead More »
I’m writing this short post mostly as a quick note on a couple of things I’m working on, after a couple of times I was asked for this kind of background.
We’re living in a world of data more than ever, and that makes it even more important to publish data following good principles of data sharing, which ease the job of finding data, …
Some Intro Reads about Lightweight Data Schemas for Life SciencesRead More »
A few notes on the work behind the conversion of the EBI Biosamples Database data into Linked Data.
Adventures with Biological Samples and Linked DataRead More »
![[MannOnto, relatedAssertions]](/wp-content/uploads/2008/02/assertion_properties.gif)
Geeez! Eventually I have submitted the thesis and given the defense presentation! My PhD project is about representing the results coming from microarray data analysis. I represent concepts like: sets of differentially expressed genes, results from clustering algorithms, claims about the role of genes in a biological pathway. I use Semantic Web technologies and an OWL model (ontology) to provide a formal representation of such knowledge. All is focused on assertions (e.g.: "IL2 is expressed under LPS infection condition"), which may be supported by experimental evidence (e.g.: a data set) or other kinds of evaluations, including ranking and comments from the users. Moreover, users and their roles (e.g.: is an expert on Immunology) may be considedered, especially for ranking the assertions. I have also developed a demo, based on the Makna Semantic Wiki.
Managing Microarray Knowledge with the Semantic WebRead More »
