So, what’s bioinformatics about?

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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.

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Some Intro Reads about Lightweight Data Schemas for Life Sciences

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Mix of standards 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, …

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Managing Microarray Knowledge with the Semantic Web

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[MannOnto, relatedAssertions] 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.

 

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