I gave my first talk yesterday at the UCD Bioinformatics Seminar Series. A couple of points. One I must remember to start using some kind of slide sharing service in order to preserve my talks. I'm impressed by the ability of others to maintain a record of their public speaking events.

The other major point that emerged from this was a discussion of Open Data and the challenges that opens up. I've already expressed an interest in hosting DAS services or Webservices on cloud infrastructure and I'll hopefully get some time to work on this in a couple of months time. I came across this article today on the topic of Open Data and it reminded me to restart a couple of data sharing projects. Hosting these in the cloud is really attractive for researchers since it dramatically lowers the costs and most of the time the amount of usage expected is lower than the pay threshold for these services.

I'll be putting the SLiMFinder code up on a svn server at some point in the near future. Hopefully that will spur some increased development of that code. There is a mailing list on googlegroups as well if people are interested.

I've been following the work of Vincent Rouilly at the Parts Registry in MIT and trying to get the DAS server dazzle working on the Google App Engine. So far it seems to work though I can't seem to get the datasources working correctly. More updates to follow.

The Advanced Interfaces Group in Manchester has been developing tools for biologists for some time. The structure viewer Cinema and tools like Ambrosia have been demonstrated to be useful in the past. I thought I would draw attention to their latest offering Utopia Documents available from here:

It's pretty powerful and for my money should be your default reader for PDF's replacing preview or Acrobat.

I've been playing around with google wave for the last month or so. I have to say I like it and am impressed by the potential. I'm interested in hearing from others interested in hooking up a Distributed Annotation System server to googlewave. I've seen some stuff about hosting a DAS server on the google app engine. I reckon this might be an interesting way to solve the writeback problem.

I've written a small robot based on buglinky to handle creating links to the ?QuickGo service from the EBI. I'd like to extend this to offer searches against the ontology lookup service and provide links to that. The robot is available at bioontorobot@appspot.com. There is also a GWT front-end to the service but this doesn't really capture the potential of the service.

Anyway - I'd be interested in collaborating on this with others interested in biological ontologies and data integration.

I have recently moved lab. Whilst I will continue to push updates to the EpiC web resource, I will not continue to use this blog for solely development related information. I intend to also draw attention to interesting articles that I have come across and to a lesser degree give an indication of the work that I will be doing at UCD. My hope is that people find it interesting and useful, but also for this to act as place for me to improve my communication skills.

So, the topic of the first post is on a couple of articles I read recently on the problems associated with being a young post-doc looking to make a name for oneself. The first relates to the culture that has arisen particularly in the UK, with which I am most familiar, that measures scientific output in terms of publications and according to some is driving people out of science and into other careers. I'm not sufficently along in my career to comment on this from a personal perspective however, I do hear this compliant often from other post-docs, the occasional young PI and rarer still from senior academics. It makes for a fairly depressing read: PLoS Biology.

The second article focuses on choosing appropriate problems for scientists. I think the paper makes some good points. Its the sort of article that people read and say that they do all the time. I think the reality is that people like to believe they do this sort of thing but don't in practice. He has a html version here for those without a sub to Molecular cell How to choose a good scientific problem.

There are a few good articles in the latest issue of Nature relating to the open sharing of data. Since the work in EpiC involves the reuse of experimental data and free access to bioinformatic programs I am quite interested in this field. Its good to see that so many people are now starting to take a serious interest in this aspect of biological research. The recent report from the CASIMIR project is an enlightning look at the problems and issues at work in sharing data. Worth a look if you are at all interested in data integration.

The Beta release of EpiC is now available in anticipation of the submission of the article. Hopefully we'll catch any little bugs before it hits reviewers. Let me know either in the comments or haslam at embl dot de.

It is available at EpiC

The main changes are to the interface and improving usuability.

EpiC was presented at the Data Integration in the Life Sciences conference in Manchester (http://www.cs.manchester.ac.uk/DILS09/). There is a proceedings paper available here: (http://www.springerlink.com/content/978-3-642-02878-6/). The conference is geared towards bioinformatic integration of a wide range of data sources for processing biological data. The slides of the talk are available here: http://www.cs.manchester.ac.uk/DILS09/presentations/Haslam-DILS09.pdf

Enjoy.

This is likely to be the last Alpha release, as we plan on publishing a paper on the service in the near future. That release will be the beta with the final release coming out next Spring. In this release the changes noted here will be publicly available. So all the feedback from the Alpbach meeting has been incorporated along with other chats with people. Nevertheless, if you see tools that you would like to see incorporated please get in touch and we'll try and get them in for the final release.