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April 2005 Archive

Havecker's Thesis Seminar Set for April 8 (4-1-05 kmw)
IGERT fellow Ericka Havecker (Interdepartmental Genetics major, GDCB Department, co-major professors Dan Voytas and Mei Hong) will present her PhD thesis seminar, Characterization of the Sireviruses: A unique group of Ty1/copia LTR retrotransposons in plants, at 10 am Friday, April 8, in 1062 Roy J. Carver Lo-Lab. The ISU computational biology community is invited to attend.

First Thursday Supper - April 7 (4-5-05 ts)
Come enjoy some conversation and food with your graduate student colleagues. Dinner will be served from 5 to 6:30 p.m. in 1102 Molecular Biology Building (MBB).

It's Time to Make Lab Decisions! (3-29-05 kmw; 4-5-05 ts)
Class of Fall, 2004 -- If you have not already done so, please email Trish to let her know which lab you've decided to join for your PhD work. MGET fellows also need to let Kathy know your plans. Please include your new office address and phone number information. Thanks!
Formalizing your Home Department -- Please download the form, Request to Establish a Home Department for Students Admitted to Interdepartmental Majors, which can be found under the heading Home Department for Students Admitted to Interdepartmental Majors on the Grad College's FORMS webpage located here.
Filling out the paperwork -- This form needs to be filled out and sent to Trish by April 14 so it can be filed with the Graduate College by April 15. Please fill out section 1, and sign it. In section II, have your new major professor sign on the Major Professor line and fill out the comments line indicating his or her agreement to accept you and to arrange or provide funding. Typically, BCB faculty have been willing to begin their financial support for students in the summer semester. So, after a discussion with your major prof, put Summer 2005 on the effective (term and year) line in the first section...If you have any questions about this process, please let Trish know ! Thanks!!!

BCB 597 to be offered Fall, 2005 (4-1-05 ts)
BCB 597, Introduction to Computational Structural Biology will be offered this coming fall semester. This 3 credit course will be taught by Dr. Zhijun Wu. The prerequisites include Math 265 and some knowledge of programming. The catalog description states: "Mathematical and computational approaches to protein structure prediction and determination. Topics include molecular distance geometry, potential energy minimization, and molecular dynamics simulation." The Registrar is putting it on the system and you should be able to register for it sometime in early May with reference #7615005. It takes place MWF at 2:10.

BCB 551 to be offered Fall, 2005 (4-11-05 ts)
BCB 551/Com S 551: Computational Techniques for Genome Assembly and Analysis will be offered Fall, 2005.

This course covers sequence alignment and assembly techniques in great depth. For example, an algorithm for computing an optimal global alignment of two sequences in linear space is developed in the course, both in pseudo code and in source code. The pseudo code form focuses on the key details of the algorithm, whereas the source code form is a complete specification of the algorithm. As a homework problem, students work out a similar algorithm, such as an algorithm for computing an optimal syntenic alignment of two genomic sequences with introns.

Students who took this course in the past told me that this course was very useful for their Ph.D. studies and their scientific careers involving analysis of genomic sequences. Students in the fall 2004 class felt that this course is very unique, useful, and reasonable in workload.

The web address for course is http://www.cs.iastate.edu/~cs551. -- Xiaoqiu Huang

News from the ISU Libary (4-1-05 ts)
Prepared by Andrea L. Dinkelman, Email: adinkelm@iastate.edu, Office: 294-6943

Web resource locator for students -- To locate quality web resources to recommend to your students, take a look at the NetWatch Archive. NetWatch is a weekly column in Science magazine. Each week Science provides brief descriptions of 4-6 high quality websites. This week’s issue features the following: Cell Centered Database; The Ovarian Kaleidoscope Database; Gateway to Lectins; and The Center for North American Herpetology. For more information: http://www.sciencemag.org/netwatch/

Have you recently published or edited a book? -- If so, please send Andrea an email with the information so she can be sure to order the publication for the collection.

We have recently received “Temperature-Dependent Sex Determination in Vertebrates” edited by Nicole Valenzuela, Assistant Professor in EEOB. Fredric Janzen, Associate Professor in EEOB has authored a chapter in this publication. Congratulations!

To review syllabi from other universities -- check out Syllabus Finder, created by The Center for History and New Media at George Mason University. The Center has created a search tool specifically for finding course syllabi posted on the Web, called Syllabus Finder. Syllabus Finder sends an optimized, specially packaged version of your query to Google, which returns the results. Syllabus Finder can be found here: http://chnm.gmu.edu/tools/syllabi/

Check out the New Titles list in Biomathematics and Bioinformatics below. -- QH 323-324 Biomathematics. Bioinformatics.

QH323.5 B562 2004 Biostatistics : a methodology for the health sciences /Gerald van Belle. John Wiley & Sons, c2004.
QH324.15 .S74 2004 Biological resource centers : knowledge hubs for the life sciences / by Stern, Scott. Brookings Institution Press, c2004.
QH324.2 .D366 2005 Database annotation in molecular biology /editor Arthur M. Lesk. John Wiley, c2005.
QH324.2 .E97 2005 Statistical methods in bioinformatics : an introduction /Warren J. Ewens and Gregory R. Grant. Springer Science+Business Media, c2005
QH324.2 I556 2004 Artificial life IX : proceedings of the Ninth International Conference on the Simulation and Synthesis of Artificial Life /edited by Jordan Pollack. MIT, c2004.
QH324.2 J66 2004 An introduction to bioinformatics algorithms /by Jones, Neil C. Cambridge, MA : MIT Press, c2004.
QH324.2 .P76 2005 Probabilistic modeling in bioinformatics and medical informatics / Dirk Husmeier, Richard Dybowski, and Stephen Roberts (eds.). Springer, c2005.
QH324.2 R35 2004 Bioinformatics : an introduction /by Ramsden, Jeremy. Dordrecht ; Kluwer Academic Publishers, c2004.

New BCB Senator for GPSS (4-05-05 ts)
Matt Wilkerson has agreed to serve as BCB’s Graduate and Professional Student Senator (GPSS). Thank you, Matt !! And, thanks to Jo Etzel for her 3 years of service to BCB in this capacity.

GPSS is not the GSB but is the official voice of graduate and professional students to the administration, undergraduates, and public at large. Through GPSS, you can have input into university issues in general or graduate student issues in particular.

In the past, GPSS promoted full tuition scholarships for PhD students (which are being phased in), better relationships between GSB & GPSS, health insurance issues, etc. Current issues include student benefits such as medical leave, vacation policies, etc.

Matt will attend monthly meetings on the last Monday of the month (except December or June). These are usually hourly meetings which take place in the Memorial Union at 7 p.m. GPSS Reps must attend all GPSS meetings so if Matt cannot attend a meeting, he will be asking for a BCB grad student to take his place. He will need to know of a replacement before the meeting so he can inform the GPSS secretary of his absence.

After the meeting, Matt will email items of interest to the BCB grad students. Announcements will also be emailed between the meetings as well.

Again, welcome to Matt and thanks to Jo !!!

Birth Announcement (3-29-05 kmw)
Congratulations to Michael Lawrence (BCB/MGET, Cook/Wurtele) and Kyongryun (Computer Science graduate student) on the birth of their son Nicholas. Nicholas arrived on December 6, weighing in at 8 pounds and 8 ounces. Our best wishes to Michael, Kyongryun and Nicholas!

April Birthdays (3-29-05; edited 1-4-07 kmw)
As April approaches, we have many good reasons to celebrate. Among these are our birthday celebrants:

    Drena DOBBS, first BCB chair
    Jennifer DONNELLY
    Ling GUO
    Ericka HAVECKER
    Tony HILL
    Vasant HONAVAR
    Matthew STUDHAM
    Michael TERRIBILINI
We also extend best wishes to our celebrating alumni:
    Sid BACCAM
    Aspen GARRY
Happy, happy birthday, everyone!

Women in Science Symposium April 1-2 (3-30-05 kmw)
This weekend's Women in the Biological Sciences Symposium, to be held from 9 am to 4 pm Saturday, April 2, in the Molecular Biology Building, will feature keynote speaker Dr. Patty Gowaty, Distinguished Research Professor in the Institute of Ecology at the University of Georgia. Her current research focuses on natural selection and variation in mating systems, sex allocation, and sex differentiated behavior.

The keynote address, The life of a woman scientist: sources of gender asymmetry in the status of scientists, will be presented at 9 am Saturday in the Molecular Biology Building auditorium. The symposium will conclude with a 3 pm poster session in the atrium.

Dr. Gowaty also will present a research seminar, Offspring viability selection and the compensation hypothesis, at 2 pm Friday, April 1, in 108 Kildee.

All are invited and encouraged to attend both the symposium and the seminar. There is no registration fee, and preregistration is not required.

Special thanks to MGET fellows Erin Myers (EEB major, Janzen/Adams) and Jennifer Deitloff (EEB major, Adams/Venezuela) for their untiring leadership in the planning and organization of this workshop.

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