Forget about Python being the prime data analysis platform: there are plenty of alternatives and R has been one of them. With CRAN, rOpenSci, Bioconductor (doi:10.1186/gb-2004-5-10-r80) the platform has three efforts where you can publish your R work. I think of them as scholarly journals: the peer review is strong with them. Anyways, over the years I did my share of R coding (a good bit of my PhD is written in R) and contributed to a few R packages. Nowadays I don't do a lot of R coding anymore.  (Sorry, genalg users: I know this package needs some serious love, and a huge thank you to those (like Michel Ballings) who have picked up the package!!)

But regarding the packaging, I still contribute my bits. For example, with rWikiPathways and BridgeDbR. So, I happily accepted the invitation to contribute to a paper that was published this week and outlines a ton of R packages that are used in the data analysis of metabolomics data: The metaRbolomics Toolbox in Bioconductor and beyond (doi:10.3390/metabo9100200), led by Jan Stanstrup and Steffen Neumann. And many R packages it discusses indeed! The paper is like an atlas, showing you around in a adventurous world of metabolomics, as clear from this dependency graph of Figure 2:

CC-BY. Figure 2 from the article.

But there is more ongoing. The article, being CC-BY is being rewritten as a book, and I have some work left to do to add BioSchemas to Bioconductor R package web pages, get more packages to use BioSchemas in their package vignettes (so the ELIXIR TeSS can automatically pick them up), and there is some more awesomeness being discussed. Well, that's not there yet, but you can start reading this metaRbolomics bible.

Thanks to everyone involved!
Posted by
Labels: Bioconductor BridgeDB BridgeDbR CRAN metabolomics R rOpenSci Wikipathways
0

Add a comment

Hi all, as posted about a year ago, I moved this blog to a different domain and different platform. Noting that I still have many followers on this domain (and not on my new domain, including over 300 on Feedly.com along).

This is my last post on blogger.com. At least, that is the plan. It has been a great 18 years. I like to thank the owners of blogger.com and Google later for providing this service. I am continuing the chem-bla-ics on a new domain: https://chem-bla-ics.linkedchemistry.info/

I, like so many others, struggle with choosing open infrastructure versus the freebie model. Of course, we know these things come and go. Google Reader, FriendFeed, Twitter/X (see doi:10.1038/d41586-023-02554-0).

Some days ago, I started added boiling points to Wikidata, referenced from Basic Laboratory and Industrial Chemicals (wikidata:Q22236188), David R. Lide's 'a CRC quick reference handbook' from 1993 (well, the edition I have). But Wikidata wants pressure (wikidata:P2077) info at which the boiling point (wikidata:P2102) was measured. Rightfully so. But I had not added those yet, because it slows me and can be automated with QuickStatements.

Just a quick note: I just love the level of detail Wikidata allows us to use. One of the marvels is the practices of 'named as', which can be used in statements for subject and objects. The notion and importance here is that things are referred to in different ways, and these properties allows us to link the interpretation with the source.

I am still an avid user of RSS/Atom feeds. I use Feedly daily, partly because of their easy to use app. My blog is part of Planet RDF, a blog planet. Blog planets aggregate blogs from many people around a certain topic. It's like a forum, but open, free, community driven. It's exactly what the web should be.

This blog is almost 18 years old now. I have long wanted to migrate it to a version control system and at the same time have more control over things. Markdown would be awesome. In the past year, I learned a lot about the power of Jekyll and needed to get more experienced with it to use it for more databases, like we now do for WikiPathways.

So, time to migrate this blog :) This is probably a multiyear project, so feel free to continue reading it hear.
4

The role of a university is manifold. Being a place where people can find knowledge and the track record how that knowledge was reached is often seen as part of that. Over the past decades universities outsources this role, for example to publishers. This is seeing a lot of discussion and I am happy to see that the Dutch Universities are taking back control fast now.

I am pleased to learn that the Dutch Universities start looking at rankings of a more scientific way. It is long overdue that we take scientific peer review of the indicators used in those rankings seriously, instead of hiding beyond fud around the decline of quality of research.

So, what defines the quality of a journal? Or better, of any scholarly dissemination channel? After all, some databases do better peer review than some journals.

A bit over a year ago I got introduced to Qeios when I was asked to review an article by Michie, West, and Hasting: "Creating ontological definitions for use in science" (doi:10.32388/YGIF9B.2). I wrote up my thoughts after reading the paper, and the review was posted openly online and got a DOI. Not the first platform to do this (think F1000), but it is always nice to see some publishers taking publishing seriously. Since then, I reviewed two more papers.
Text
Text
This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
About Me
About Me
Popular Posts
Popular Posts
  • ChEMBL 09 as RDF
    Update 2021-02: this post is still the more read post in my blog. Welcome! Some updates: Ammar Ammar in our BiGCaT group has set up a new SP...
  • Converting any SPARQL endpoint to an OpenAPI
    Converting any SPARQL endpoint to an OpenAPI
    Logo of the grlc project. Sometimes you run into something awesome. I had that one or two months ago, when I found out about a cool pro...
  • Data duplication at Mendeley
    Data duplication at Mendeley
    Earlier this year I gave Mendeley a try, after having been a happy JabRef user, unhappy Connotea user (main problem was that any URI can ...
Pageviews past week
Pageviews past week
2118
Blog Archive
Blog Archive
Labels
Labels
Loading
Dynamic Views theme. Powered by Blogger. Report Abuse.