Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, discussing and comparing different offerings like Pipeline Pilot, Taverna, and KNIME.

Userscripts
The paper on userscripts describes how Greasemonkey scripts can be used to combine different information sources (DOI:10.1186/1471-2105-8-487). A trailer:
    Background
    The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This pens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources.

Peter et al. have been using this technology for CrystalEye too, but the paper was in a finalizing state when the userscript was announced, unfortunately.

Bioclipse 1.2.0
The other present is the Bioclipse 1.2.0 release, for which the QSAR feature is a great new feature addition (see my blog the other day with an overview of blog items detailing my participation in that feature). Ola et al. have done a great job with the plot functionality, which is very nice to scatter plot calculated descriptors. This release is likely going to be the last one in the Bioclipse 1 series, except for bug fix releases, so, this release also means I can start contributing to the Bioclipse 2 series. Recent items in the Bioclipse blog show a bright future, with project based resource handling, better scripting (R, ruby, JavaScript, BeanShell?).

BTW, we never have presents under the tree; we have Sinterklaas.
Posted by
Labels: Bioclipse bioinformatics CDK chemoinformtics KNIME QSAR R scripting Sinterklaas Taverna
5

View comments

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...
  • CDK Module dependencies #3
    CDK Module dependencies #3
    Jonathan is here with me to work on his fingerprint project. He asked about CDK modules, which we use to control dependencies, within the ...
  • 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
37904
Blog Archive
Blog Archive
Labels
Labels
Loading
Dynamic Views theme. Powered by Blogger. Report Abuse.