First BiRG Meeting of 2008

BiRG will hold its first group meeting of 2008 at 5pm on Friday, 11 January in LF 264. All are welcome.

Scientists map imprinted genes in human genome

Article, from December 3rd issue of Genome Research, details Duke University study that used machine learning to identify
imprinted genes in the human genome.

http://www.physorg.com/news115623039.html

Interesting links for BiRGers

Loads of Animations : http://science.nhmccd.edu/biol/bio1int.htm

Interactive Sequence Alignment http://helix.biology.mcmaster.ca/chpt7.pdf
Kimura 2 parameter Model http://helix.biology.mcmaster.ca/chpt8.pdf
Information Theory w.r.t. DNA http://helix.biology.mcmaster.ca/chpt10.pdf

Interesting Animations

PCR  http://www.geneticorigins.org/pv92/aluframeset.htm
Transcription http://www.youtube.com/watch?v=mQClpqDBlSs
Translation http://www.youtube.com/watch?v=YURu6lv7I6c&feature=related
Synthesis http://www.youtube.com/watch?v=NJxobgkPEAo&feature=related
Retrovirus (parasite view) http://www.whfreeman.com/kuby/content/anm/kb03an01.htm

Alu Theory

Basic Alu Paper
http://www.geneticorigins.org/pv92/aluframeset.htm
http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PLEEE8000074000002022901000001&idtype=cvips&prog=normal
http://www.ufrsdv.u-bordeaux2.fr/siteIML/Maste2biosante/Master2biosantecours/articles/AdG-28sept-Dewannieux.pdf
http://www.jstor.org/view/00278424/ap990245/99a00420/0
Selection of Alu sequences
Alu Poly A tail
Alu 225 new genes

Nov 23 - Interesting Talk

Next week (November 23) our visiting graduate students will be presenting on local and global sequence alignment concepts.

Dr. Michael L. Raymer: Thursday, 1st November

Dr. Michael L. Raymer will be delivering a talk at IUS on Thursday, 1st November 2007 at 12:15 in LF348. There will be punch and pie.

Interesting Linguistics/Informatics Article

Read about the evolutionary "regulation" of verbs:

http://www.sciencecodex.com/harvard_scientists_predict_the_future_of_the_past_tense

13th Annual Indiana University Undergraduate Research Conference, Friday, November 30, 2007 at IUS

The 13th Annual Friday Indiana University Undergraduate Research Conference will be held on November 30, 2007 at IU Southeast.

Participate in an informal roundtable, share a poster or present an oral paper. Share your research with other undergrads throughout the IU system.

Abstracts (200) word for The Indiana University Undergraduate Research Conference should be submitted to Dr. Ramachandran by Thursday, 11 October.

September 28, 2007 BiRG Lab Meeting

Agenda

• October 5th: NSF Day at Buter University
• October 19th: Statistics Every Informatician Should Know, Part I
• Perl Basics Presentation by Shawn Hanes

BiRG Trip to NSF Day at Butler University

On Friday, 5 October, 2007, BiRG will be traveling to Butler University in Indianapolis, IN for NSF Day. We will meet at 4:45am in the parking lot just outside of the Life Sciences building and plan to arrive at Butler at 7:15am.

Statistics Every Informatician Should Know

On October 19th, 2007, Professor Manwani, BiRG Statistician, will present an introduction to statistics that every Informatician should know. Please feel free to stop by The BiRG Lab (LF264) at 6pm for the presentation. All interested parties are welcome to attend.

Shawn Hanes Presentation on Perl Scripting

Common Experience Competition

Indiana University Southeast's Common Experience Competition presents an exciting opportunity students to share essays, poetry, research papers, dimensional art pieces and/or photography illustrating one's identity in a multi-cultural world.

Cash prizes of $300.00, $200.00 and $100.00 will be awarded.

This is an opportunity to win money for The BiRG by approaching from the perspective of a Social Informatician.

See http://www.ius.edu/commonexperience for more info.

September 21, 2007 BiRG Lab Meeting

Agenda

• Dr. Michael Raymer will be visiting on November 1st
• BiRG lab meeting will be held on Thursday, November 1st instead of regularly scheduled Friday meeting
• Presentation: Junk DNA by John Lannon

Dr. Michael Raymer To Visit IUS on November 1st

Presentation: Junk DNA by John Lannon

Click here to download Powerpoint presentation

September 14, 2007 BiRG Meeting

Agenda

• New BiRG PCs Acquired
• Printer Still Pending Setup
• Mutation & Evolution Discussion

Three new BiRG PCs

Thanks to the efforts of Dr. Ramachandran, Dr. Hollingsworth and Shawn Hanes, BiRG now has 3 fully-functioning research machines running Ubuntu, Censor and WU-Blast. Additionally, an Unbuntu-powered general use machine and an IBM integrated Monitor/CPU running DamSmallLinux are available. BiRG still also has its original two Windows machines for general research use. The 3 special purpose research stations are:

• DNA - for John's research project
• RNA - for Shawn's research project
• Protein - in progress

And, then there's:

• Mutation - practice Linux machine; training dock for new BiRGers
  

Mutation and evolution discussion

Stay tuned for update

Freely Available Online Course Materials

Thanks to MIT's OpenCourseWare, anyone with an internet connection can freely access course materials (homeworks, recitation assignments and lecture notes) to many of MIT's courses. If you're interested in Computational Biology, check out course 6.895.

Or, if you just want to browse the offerings, check out OpenCourseWare.

Furthermore, MIT's Stellar Course Management system (based on The Sakai Project, like our very own Oncourse CL) also allows public access (with registration) to many current courses.

416Gb Solid State Drive Announced

For those of us interested in emerging hardware trends, Engadget today profiled a recently announced product by BiTMICRO: a 416 Gigabyte SSD (or solid state drive) in 2.5 inch form factor. This means 416Gb of storage with no spindles, no needles, essentially, no moving parts. Lightning fast access times and fewer moving parts means that motherboard manufacturers better step up and fatten up their busses ASAP.

New Books Available in BiRG Lab

Dr. Ramachandran has made available two new books for general lab use:

Book 1: BLAST
Book 2: Beginning PERL for Bioinformatics

Please keep in mind that general BiRG lab resources are to remain in the lab (LF264) at all times. Please do not remove them from the lab.

Posters on The Hill Announcement

Call for Abstracts to Posters on the Hill 2008:

It is increasingly important that the scientific community works to ensure that those in the U.S. Congress who provide funding for science and science education have a clear understanding of the programs they fund and why these programs are important. Undergraduate research must be among those programs that members of Congress understand if it is to continue to be supported.

Nothing more effectively demonstrates the value of undergraduate research than the words and stories of the student participants themselves. In the Spring of 2008, CUR will host its 12th annual undergraduate poster session on Capitol Hill. This event will help members of Congress understand the importance of undergraduate research by talking directly with the students whom these programs impact.

CUR is calling for students to submit an abstract of their research that represents any of CUR's divisions (Biology, Chemistry, Geosciences, Mathematics/Computer Science, Physics/Astronomy, Psychology, and Social Sciences). We are also accepting abstracts in the Humanities. In honor of International Polar Year, the Council on Undergraduate Research would like to encourage the submission of research abstracts for Posters on the Hill that involve polar research.

Posters on the Hill is tentatively scheduled for April 16, 2008 in Washington, D.C. The deadline for submitting applications is November 15, 2007. More information and the application are available at: http://www.cur.org/postersession.html.

September 7, 2007 BiRG Meeting

Agenda

• John Lannon awarded IUS undergraduate fall fellowship
• BiRG accumulates new books and other resources
• Posters on The Hill deadline November 15th
• Change of schedule for September 21st presentation
• Professor Manwani to present a statistics primer on October 19th
• Presentation on IUS library resources by Theresa Butler

John Lannon receives undergraduate fall fellowship

On Thursday of this week, BiRG member John Lannon was awarded an undergradate fall fellowship to carry out research on Alu distribution across
the human genome.

BiRG accumulates new books and other resources

Dr. Ramachandran has made available a large assortment of textbooks and articles
for general lab use. A locker has been provided for BiRG member use. BiRG is
also in the process of acquiring its own computing resources to support and
bolster our research efforts.

Posters on The Hill

Posters on The Hill is an opportunity for undergraduates performing research
to share their ideas with U.S. Congress. The deadline for abstracts for submission
is November 15th. Read more about Posters on The Hill.

September 21st presentation change of schedule

Instead of presenting The Human Genome Project on September 21st, John Lannon will be using this time to introduce the group to his research project on Alu sequences. Thomas House has tentatively agreed to present the Human Genome Project primer on October 12th.

Professor Manwani, BiRG Statistician, to present statistics primer

Professor Manwani, BiRG's Group Statistician, will be presenting a primer on statistics during out October 19th lab meeting.

Theresa Butler presents the vast resources available via The IUS library

Theresa Butler introduced BiRG to the many online and offline resources available to students via The Indiana University library system. Check back here for more notes and links.

Human Genome On The Radio

On today's Science Friday, an National Public Radio show discussing current science topics, host Ira Flatow and guest, Huntington Willard, the director of The Institute for Genome Sciences and Policy at Duke University, discuss the recent publishing of scientist J. Craig Venter's entire genome (well, at least 96% of it). Check out the Podcast here.

BiRG Member Awarded Research Fellowship

BiRG member John Lannon was awarded today an Indiana University Southeast Undergraduate Fall Fellowship to carry out research on Alu distribution across the human genome.

Lannon will be presenting the results of his research at the IU Southeast Student Conference, Celebrating Achievement, in April 2008.

For more information regarding the project, please attend BiRG lab meetings in The Life Sciences Building, room 264 on Friday evenings at 6:00pm or email iuse.birg@gmail.com.

BiRG Message Boards Launched

BiRG member Shawn Hanes has been gracious enough to host a phpBBB-powered message forum for the group. This forum will allow the group to correspond in a group context and will allow us to better share ideas, research and questions.

The forum can be found at http://birg.slackzer.net.

Biologist Craig Venter Publishes 96% of His Own Genome

As reported by CNN.com today, Biologist and entrepreneur, J. Craig Venter, has recently published 96% (6 billion letters) of his own genetic code in the journal PLoS Biology. Venter was the head of Celera Genomics, a private company that concurrently worked on mapping the human genome alongside The Human Genome Project.

The article can be found here.

Furthermore, a direct link to the publication in PLoS Biology can be found here.

BiRG Calendar Available Online

The BiRG calendar is now available online via Google Calendar.
Click the link below to check it out:


Furthermore, one can subscribe to the calendar via iCal (or an iCal compatible application for Windows or Linux) via the following link: [iCal]
OR
An XML feed: [XML]

August 31, 2007 BiRG Meeting

Agenda

• Suggested topics for upcoming presentations
• Schedule for future presentations
• Grants available for BiRG
• BiRG Informatician position available
• BLAST presentation by Theresa Butler
• Discussion of potential research projects

Suggested Topics for Upcoming Presentations
Dr. Ramachandran began the meeting by suggesting the following topics for future
presentations:

• Perl programming basics (to be presented by Shawn Hanes on September 28th)
• Censor (a program for identification and elimination of repetitive elements
  from DNA sequences)
• Human Genome Project (to be presented by John Lannon on September 21st)
• DNA basics (to be presented by Leah Balmer on September 14th)
• NCBI introduction (National Center for Biotechnology Information)
• BioInformatics primer
• IUS library resources (to be presented by Theresa Butler on September 7th)
• IUS computing resources

Schedule for Upcoming Presentations

September 2007

• 09/07 - IUS library resources, presented by Theresa Butler
• 09/14 - DNA basics, presented by Leah Balmer
• 09/21 - Human Genome Project, presented by John Lannon
• 09/28 - Perl programming basics, presented by Shawn Hanes

October 2007

• 10/05 - Open (conference at Butler University in Indianapolis, IN)
• 10/12 - Open
• 10/19 - Open
• 10/26 - Open

November 2007

• 11/02 - Open
• 11/09 - Open
• 11/16 - Open
• 11/23 - Open
• 11/30 - Open

December 2007

• 12/07 - Open

Grants Available for BiRG

• Large grants: 4 available (up to $1500 per semester) for Spring 2008. Priority given to those with defined BiRG positions
• Small grants: several available (up to $500 plus travel expenses)

BiRG Informatician Position filled by John Lannon

BLAST Presentation by Theresa Butler

Theresa and Dr. Ramachandran introduced the group to NCBI's Basic Local Assignment and Search Tool (BLAST). BLAST is a program accessible for free at http://www.ncbi.nlm.nih.gov/blast/ that allows one to search all of the available genetic sequence databases. One can start with a protein or DNA sequence and find similar results based on several sophisticaed heuristic algorithms. This presentation served as an introduction to just one of the freely available genetic information tools that will prove invaluable to BiRG members in the future.

Discussion of potential research projects

Dr. Ramachandran discussed potential research project ideas with members. Among the discussed topics was molecular evolution and, in particular, the evolution of specific retroviruses.