Monthly Archive for April, 2010

Happy DNA Day!!

Happy DNA Day!!

This past March, we had a great time participating in the science programs in San Diego. We ended the month with the SD Science Festival with over 30,000 participants. It was such a busy day – I forgot to take pictures. The venue was Petco Park with hundreds of exhibits and hands-on experiences. We had our sediment batteries and microscopes.

With the thaw in Maryland from the multiple snow storms, April is beginning to show signs of spring including the Rockville Science Day. This will take place this Sunday, April 25 at Montgomery College, Rockville Campus. We should be easy to find – look for a big black bus.

In addition to the spring festivals and our school visits, behind the scenes we’ve been busy reviewing/selecting interns and setting up our summer professional development schedule. We had over 360 applicants this year to our internship program from all over the US and world. The blizzards this winter didn’t hold back the applicants. Notifications were be emailed to all on Friday, April 16th to the email address provided on the application. The applicants were so impressive!! Unfortunately we are not able to host everyone.

Our professional development programs were announced this month with support from Life Technologies Foundation. We are fortunate to be able to partner with such generous sponsors to bring these programs to fruition. We are REALLY excited about this year’s programs. They are filling up. California is almost FULL – be sure to send your application in. Maryland has room still – but don’t delay.

On that note, the Genomics Course for Educators on both coasts have biodiversity as the research theme. Our understanding of the diversity of life barely scratches the surfaces (literally). There are so many bacteria on and in our planet, not to mention our bodies – we are just beginning to know they exist – let alone, understand their significance. Even in our macro world, not every species has been catalogued! So much work to be done!!!

We are partnering with the Canadian Barcoding of Life Network with several other organizations in the MacArthur HASTAC Digital Media and Learning Competition. The project is to develop a fun science social networking site to encourage students to participate as citizen scientists and participate in developing a digital list of all organisms around the country and world. Please review the video at the link below and provide comments. It is important that the comments are added via the HSTAC site – the YouTube comments do not carry over. These comments are used in the decision making for funding.

Thanks for your support!!!

And, again, Happy DNA Day!!!

Recomb – Computational Proteomics

I recently attended the Recomb satellite conference on Computational Proteomics (downloads for talk and poster) in San Diego, CA.  It was a kind of homecoming for me.  I was a computational proteomics researcher at UCSD as a grad student with Vineet Bafna.  Many of my classmates were still there, as were lots of familiar faces and friends.  I joked with Marshall Bern, that this was almost all of the people at ASMS that I wanted to hear gathered in the same room, and it was only two days. Oh, and there was a beach.

Revisiting computational proteomics was a lot like hearing an old high school favorite on the radio.  You sing along with the chorus and then mumble through the verse.  But by the end, you remember it all again.  Having diversified my research interests while at JCVI, I was excited to hear new developments in proteomics, as well as get a refresher on some oldies-but-goodies.

I presented the progress on my proteogenomics research, introducing some comparative proteogenomics. I submitted a poster abstract, and was asked to give a “flash-presentation” during the Saturday session as well.  As the attendees were like-minded geeks, I presented my troubles spots as well as the highlights, hoping for advice and suggestions.  For highlights, we have the pipeline running smoothly on the JCVI infrastructure, and can analyze any LTQ dataset rapidly.  This produces a list of genomic loci needing re-annotation.  I have somewhere around 10 datasets done now, and they all have been informative. Each shows a significant amount of gene novelty. As we amass a more diverse set of results, we are starting to look at the annotations from a comparative or evolutionary standpoint.

For trouble spots, I noticed that larger datasets need more attention to downstream processing.  You can’t simply claim that all ‘novel’ peptides are new genes. First, we require high quality PSMs (p< 0.005 ) and then do a fairly detailed analysis of results.  I found that even with very strict PSM filters, there were a significant number of false-positive ORF identifications.  For this I have started to develop ORF level filters that look at the set of peptides in an ORF and not the individual ORF identification.  You could, as Pavel suggested to me, go with perfect ‘zero FDR’ at the PSM level, but that tends to kill your spectrum identifications to the point where you see very few novel results (slide 6 from the talk).  I feel that a more sensitive approach is to introduce the orthogonal filter (ORF level).  I hope that later this summer I’ll be able to get out a Nature Methods paper about all the lessons learned.  Till then …

A Positive Charge

I’m thinking of the day’s schedule school visit, the activity and the positive charge it will produce in me and the students.  I get so excited during our school visits.  It’s like the feeling I get on Saturday morning while watching my favorite cartoons. (Yes, I still watch cartoons)  The first class I ever taught was at Hine Jr. High School in Washington D.C. in 2005 and the activity was Mystery of the Crooked Cell. 

After the classroom visits,  the Science Fairs, After School Programs, NIST Adventure in Science and Take Your Child to Work Day programs, in this my 5th year as Mobile Lab Driver and Teaching Assistant, I still get excited when working with a group of students.  I’m the preverbal kid in a candy store with the keys and I even make the candy!

 As I ponder this, another thought comes to mind, in our effort to reinforce specific standards of science and exposure to FUN!  I have come to understand the importance of the program and the positive charge on students, teachers and the community.  In a time of educational cut backs, the layoff of teachers and the closing of schools, the DiscoverGenomic! Science Education Program is a sure sign that we have not left any child behind.

Thanks for a positive charge DG! Science Education Program!