Systems Biology Research Blog

I'm totally convinced that a key of successful cooperation in science is the sharing of information. This issue needs to employ collaborative software to communicate and share data, which I summarised some years ago (see my somewhat outdated poster). A more actual approach to collect and, more important, categorise some of the technologies is done by [citet]Romano2011[/citet]. I'm aware that the authors have to balance on the border line of mention the most useful tools for bioinformatics and the danger of a messy link archive. I also totally agree that the missing inter-connection between the tools (not just the mentioned networks) is the biggest problem right now. On the other hand, I think the article is not paying enough attention to the exchange of scientific publications. Inside a spatial distributed project group, this may become a distinct issue. In particular I missed a notification of Bibsonomy [citep]Benz2010[/citep], which I presently test.
Among public sharing, the website allows to store publication lists for private or group purposes. It also includes a pretty number of export options, so that collaborators can use them in their desired way. Using the provided JabRef-plugin, the synchronising of local stored publications and the website is simple. But it is noteworthy, that there is still potential for improvements. For example no subgroup-function is implemented and the JabRef-plugin offers only options for private or public visibility, but not for group wide visibility. Presently I use the JSON export function of Bibsonomy in cooperation with JabRef and a render plugin to easily create reference lists for blog posts (later more when the plugin is working like a charm).

Picture: Alan D. Wilson, www.naturespicsonline.com, Copyright: CC-Attribution-ShareALike 3.0

Last time I was excited about the Monty Hall Problem. Accidentally I read a blog post dealing with pigeons and referring to [citet]Herbranson2010[/citet] where the authors analyse the performance of pigeons to solve this puzzle. Compared with former published studies, the pigeons outperform human test candidates. Very fascinating topic. Now I want to see a competition between budgies and pigeons.

You ever heard about the Monty Hall Problem? Here you can test it empirical: The Monty Hall page. Sometimes mathematics frighten me.

It isn't a secret that one basic prerequisite in any research is to be up to date by reading the newest publications. To get knowledge of a new article, journals offering email alerts. The interdisciplinary character of Systems Biology causes a fragmentation of publications to a number of journals. Journals dedicated to biology, physics, mathematics, computer science or a combination of it, may publish articles related to Systems Biology. However, if I would subscribe to all of the offered email notification my mailbox will be flooded. Thats why I prefer RSS feeds. Since I updated my laptop to the new KDE4 desktop, I use a plasmoid to get notified for new articles (see screenshot).

The KDE Desktop includes a plasmoid (widget) to read RSS feeds. It allows to stay updated with the newest research issues.

Unfortunately it's not always easy to find a feed from the publisher website. That motivates me to investigate the provided web feeds of some major journals related to Systems Biology. The results varies from a valid feed containing the abstract to no feed at all. Additionally I'll offer an OPML file containing the RSS feed for an easy import to an appropriated feed reader.

Full story »

New year, new content. Since I'm seriously busy due to my study, my blog became more and more orphaned. There weren't also that interesting things, which I could use to fill posts.
Therefore I decided to start a new sub-blog related to Systems Biology, where I can combine three things:

1. Update my blog regularly
2. Support my research
3. Improve my language skills

Because research is every time international, the content will be mainly in English. (Sorry Thomas...) As the title of the blog and the foregoing words already describe, my field of interests is the research in Systems Biology. I'm not willing to explain the basics of it, but in my daily work I notice interesting and often useful things, e.g. papers, tools or websites, and because I'm a fan of transparent research, I'll publish these finds.
Last but not least: I wish you a happy new year!