nodalpoint.org

The last chapter of Craig Venter's version of Celera has been written. Via Universal Acid: Celera has given up trying to sell genomic information. The end result is that all their genomic data will be put in the public domain. Which is I guess, a good thing...

As much a reminder to myself as a spur for the rest of you...

Can it be the end of April already? Where does the time go? More importantly, get thinking about your next submission for "Bioinformatics paper of the month" in 2 days time.

Hello World.

I Have a question for the fine people here, and I am a rank amateur, so please excuse my lack of proper vocabulary.

I've been trying to find the whole story on a case which I read about several years ago- I think it was possibly in John L. Casti's "Paradigms Lost", or possibly Stephen Pinker's "The Language Instinct".

In any case, the example refers to a "famous experiment" which is often referred to as "[so-and-so's] Monster", in which, a microorganism is placed in an extremely hospitible environment and allowed to thrive there with no enemies or inhibition. After many generations of reproduction in this safe environment, the organism was found to have a markedly less-complex genetic structure.

I am a high school student in tenth grade and my teacher has asigned an assignement where we have to find pros and cons (or positives and negatives) of using bioinformatics. If anyone could help me with this information it would be greatly appreciated. Thanks,
Tbone

With the announcement last week that LION is planning to sell off its bioinformatics business including SRS, a lot of labs are or will be looking for new ways to handle biological data integration. For those not familiar with SRS it is software package that parses and indexes the majority of the biological data sources that exist today and allows you to search all of them through a standard interface. It has the ability to use links between data sets to pull lots of disparate pieces of information together in result sets and generally eases a lot of data warehousing problems. SRS is a commercial product but is available for free to Academic institutions and non-profits. So the question I would like to pose to the nodalpoint community is what have you found to work for your data warehousing needs? Read on for more about data integration...

Any ideas on how to increase nodapoint's Google-hits?

Are there commercial opportunities available for providing computational services for small companies without financial resources to establish an in house wet-lab?
The semiconductor industry has an established model of fabless chip design companies. Are we going to see a similar model in the drug or enzyme design industry any time soon? From searching on the Internet I do not get the impression that such a business model prevails today. What are the barriers we need to over come before such a model becomes successful the same way as the fabless chip design model has prevailed?

As many of you are probably aware the officially supported nodalpoint Linux distribution is Debian. Seriously though, most of our regular contributors are Debian users and we can probably thank Dopey for setting us straight (orignially I was running nodalpoint point on a RedHat server). Now there are many reasons why Debian is a better choice than RedHat for use in an academic environment (security, flexibility, package dependencies etc.). There are also good reasons why you would choose to run RedHat over Debian in a commercial environment, the main one being support contracts from commercial vendors like IBM. This thread over at slashdot on Using Debian in Commercial Environments is a good roundup of the issues involved. The consensus seems to be "Don't run Debian if it voids your support contracts with IBM".

So now I am faced with a similar situation. My current lab has purchased the Tivoli backup system from IBM and of course the only supported platform is RedHat. So my question is should I give up my Debian web server in favor of RedHat so the IBM engineers can install the Tivoli access manager or should I deal with the installation myself using alien ? I find this situation rather annoying (for selfish reasons maybe ?) but we are in an academic environment and not a commercial one. It makes sense to me to save money implementing our own backup solutions and use the grant money to hire more people ?

The editor(s) of Scientific American has one, Science magazine has one, I have one. That's right people, be prepared for the rise of the academic weblog.

So far the numbers are small and the range is diverse, however the theme is definitely scientific. You can read researcher's takes on anything from developmental biology, boolean networks for modeling cancer, anthropology, mass spectrometry, genetics of human migration, Archaea, and even systems biology. Click on the "read more" link for my current reading list...

Update: I have added all of the blogs mentioned to the recommended reading list (block). For suggestions or additions please add a comment to this thread.

Maybe it is an indication of how sad I really am or that I have taste, but I have never seen a single episode of American/Australian/British or any other "Idol" show. But I do remember Star Search and the concept doesn't seem that different. So I can only imagine some genius at Channel 4 decided that "wouldn't it be a good idea to have Science Idol" i.e. find the next David Attenborough using reality TV. The series is called Famelab, the The Guardian has more.