Monthly Archives: September 2008

Medline Cognition : Pubmed searches using Semantic Natural Language Processing

I came across a submission to Nature Precedings this morning detailing the creation of a “semantic – natural language processing ” based search for the Pubmed database by Cognition Technologies  in collaboration with a team at the Department of Biochemistry at UT Southwestern Medical centre in Dallas.

A few searches later, I can definitely say the technology that drives “Medline Cognition” works and works extremely well. 

The Cognition paper details the creation of its “semantic map” involving many manual steps and the improvements to existing curations, indexes and ontologies.  The final result is its Medline concept index that drives its semantic search.

The paper has a brief comparison of its “Medline Cognition” searches compared  to PUBMED searches.  I too tried a few searches and can definitely say that unlike the other semantic web offerings that have been hyped recently, the patented-platform being built ( called CSIR)  works very well and can only get better as suggested by the planned improvements  detailed in their Nature Precedings paper.

Work on things that matter : Tim Oreillys keynote at Ignite Boston-4

I have been to three of the four Boston ignites and even spoken at the second one, but yesterdays keynote by Tim oreilly at Bostons Ignite-4 was truly exceptional . It takes someone with Tim Oreillys vision to put it the way he did. It was one of those talks you walk away from inspired and I am afraid my summary will not do it justice. But I am forcing myself to try by writing down what I took home from his rousing talk

jHere are the key points

# Alphageeks matter , they are the look of things to come , todays Pioneers

#Global warming is real , and even if you dont believe in it , taking action will only benefit us

# Its time for us to come-together to work on problems that matter and that make a difference. And there is no shortage of problems that can use an alpha-geek outlook

# The sensor-web is here , this is a collection of sensors that abound in our digital lives, be-it the GPS receivers , TPMS ( tyre pressure monitoring systems) or the ubiquitous cell-phones . Sensors are getting cheaper and cheaper and they are all linking with each other to capture data that should be put to uses that could benefit us all

# Be it education , alternative fuels , ecology or social empowerment there are numerous opportunities for us to act and connect with others out there who are toiling away at their niches struggling to make a difference

# Everyone should register to vote and do so ! We owe it to ourselves and our futures

If you can catch a video of the talk , do so! Its worth the few minutes of your time

A messy world indeed: 64 bit runtimes , 32 bit browsers

I was going to title this post  “64-bit , 32-bit , Java plugin, Java 1.6,  Leopard Tiger , grrrrr”  and even though that title sounded like a bunch of keywords thrown together , that effect was entirely intentional.

I have just spent half an hour trying to troubleshoot why JAVA plugins stopped working on my Mac Pro at work and I am very very confused!

And I absolutely need Java plugin support because a lot of the protein visualization apps like JMOL @ Mole Online use the Java plugin very effectively. And before I launch into my rants , a Disclaimer, everything works great in Safari and I guess I have no right to complain!. But I just like Firefox so much ! ( sometimes I wonder why)

SO here are the issues as I see it

1) The Mac Pro is a through and through 64 bit OS ( Or is it! , there is some 32 bit Carbon lurking in Firefox and other apps I hear )

2) Safari 3.0 on the Mac Pro is probably 64 bit ( Clarifications sought)

3) The default Java plugin and Java runtime on Leopard are  Java 1.6

4) Firefox 3.0 , which I downloaded from the web is probably 32 bit

5) I dont know why Firefox cannot gracefully degrade and use the old 32bit plugin. I still see it installed and available as an option in my “Java Preferences”

All of this probably indicates the confusion behind 64 bit platforms in my mind and the minds of other consumers like me . It also explains why 64 bit adoption continues to be so slow despite many years of talking about it.

Naively I wonder  why everything and everyone cannot just wake up and be 64 bit!.

Even though I am quite annoyed by my mornings experiences, a google tech-talk from Kenneth Russell , and several comments on the Java Posse episodes in AUgust 2008 suggest that a lot of change is coming soon with the new Java plugin which is going to be part of Java 6 update 10.

Well with todays frustrations , I cannot wait!

Hopefully that will allow a 32bit applet to run on a 64bit plugin runtime in a 32 bit browser! Can they make this any more confusing?