Associate Professor Informatics @ Indiana University, Bloomington- Andrews-Dalkilic Laboratory @ Dept. Biology Indiana University, Blooomington
- Associate Director Bioinformatics @ Indiana University, Bloomington
- Project Leader Center for Genomics and Bioinformatics
- Adjunct Assistant Professor Computer Science
- AGEP Faculty
Current PhD and Masters students
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James Costello is working on Indigene which is an applied systems biology project combining genome-scale data for Drosophila m. Jim is co-advised by Justen Andrews in the Dept. of Biology and Drosophila Genome Resource Center (DGRC). -
Scott Beason is working on Electronic Health Records. He has had extensive experience working at Microsoft, Price Waterhouse, and several start-up companies. He is also interested in large software projects in C# -
Chingqing (Andy) Lin is working on discovery in chemical and systems biology (Indigene) networks. He is currently on hiatus working for Oracle right now and making bank
Met with Dirk and Yu-Wei and Zn-Fingers.
Academic Council Meeting
Review PhD and Master's admissions
Review entries in Springer's Database Encyclopedia
Facutly Meeting (Informatics)
Speak with Dean, Chair, and Academic Council on four issues--meeting was short because of extenuating circumstances
Wedding
Kan and I had a wonderful walk
Still reviewing for ISMB--I'm late, but at least I'm thorough.
The Tundra is beautiful
I miss someone, but I'm not sure who.
Met Eric
I worked out from 5:15am to 6:30am last week--i'll run afterward too
"Only the little IOUs count," from my Dad.
- 3:31 PM
Completing Encyclopedia entries
Working on VLBD with Dan
Examining Zn-finger nucleases
Do you know what "perdurable" means?
From slashdow=r The detection of planet HD 189733b is in some ways just another small victory for extra-solar planetary science.
Reservoir Hill writes "An article from last week runs down the new mass audience for gaming among families, women and older people. The importance of the mass audience in gaming's spectacular growth is seen most clearly in the success of Nintendo's Wii, which is far outselling its more technically advanced hardware competitors, the Xbox 360 from Microsoft and PlayStation 3 from Sony. Wii Play was the No. 2-selling game of last year even though it received an abysmal score of 58 out of 100 at Metacritic, which aggregates reviews. The Times says that as video games become more popular hard-core gamers are becoming an ever smaller part of the audience. 'Paradoxically, at a moment when technology allows designers to create ever more complex and realistic single-player fantasies, the growth in the now $18 billion gaming market is in simple, user-friendly experiences that families and friends can enjoy together.'"
An excellent article on computer education
Completed Business Use Case Symposium and course work.
A very interesting article in Nature Vol 451(7) 2008, Evolution of anatomy and gene control, George Koentges.
- (edited February 13, 2008, 8:45 AM)
Do you know the word, "raiment?"
Two weeks to draft Mentor/Mentee letters
Here's a nice opportunity:
Postdoctoral and Predoctoral Fellowships in Biomedical Informatics, Vanderbilt University
The Department of Biomedical Informatics at Vanderbilt University is currently accepting applications for Fall 2008. Highly qualified candidates may apply through the end of this month.
Offering M.S. and Ph.D. degrees in Biomedical Informatics, as well as nondegree postdoctoral training, this National Library of Medicine-funded training program has a limited number of full fellowships (including tuition, stipend, health insurance, travel allowance) available for U.S. citizens or permanent residents.
For more information about the program and the application process, please visit our website at Vanderbilt or contact Claudia McCarn, Administrative Manager of Educational Programs, at Claudia.Mccarn@Vanderbilt.edu.
P & T
Dan [with] Ontologies
- 6:56 PM
Transfer Credits for Ankita
Create report for space Current Supported Students
Accepted From protein-disease associations to disease informatics In Frontiers in Bioscience
Meet with MeadJohnson
Meet with Whirlpool
Meet with Indigene Team
Submit to ISMB
Submit to Springer-Verlag's Encyclopedia of Database
Submit to PODS
Submit to FLY
Submission in progress to Genome Biology
Working through PhD applications
Speak @ Medical School Feb 4, 12:00-1:30pm
Trustees meeting Feb 6 1:00pm-4:00pm
Meet with Yu-Wei on Zinc-finger problem
Meet with Dan on Environmental Ontology - (edited January 30, 2008, 9:32 AM)
Faculty meeting on Friday. The reports from the strategic planning committees. Not sure I understood all of the outcomes, since the verbal reports seems somewhat different from the written. I did object to lumping Bioinformatics inside "Life Sciences". I imagine escience is the grid computing. What came as an interesting outcome was "Technology for Values", though a suspect a fair number of us are still unsure on a number of levels what this actually is.
Indigene meeting was a smashing success--our integration is working and everyone is estatic.
We have a meeting with MeadJohnson in mid January.
Scott and I are attending a Requirements workshop for best practices.
Jean had a nice holiday gathering, as did Peter.
Our academic council was envoked, though I'm not sure if there was an outcome.
My first Gen. Ed committee was devoted to voting on less than six items, two of which were tabled because of confusing phrasing. I'm not sure if it's possible to have a roomful of PhDs and not find some group who'll find something ill-phrased. I've electronically voted--my intent was to make more classes more available--especially after the reports of the honors students.
The H101 class was a blast! One of the best experiences I had. Our final project was a short paper and presentation on a problem each student found (unexpectedly) important (these are not listed in any order)
(1) Jeff Capati (Senior Honors) examined injuries/cost of profession sports and how to anticipate and reduce this problem
(2) Charlie Clark discussed how difficult registration is for honors students--he (a pre-med) student finds it both discouraging and frustrating to have had to be waitlisted for three times for a basic chemistry class. His solution to was prioritize based on a number of criteria including GPA, standing, and even SAT ACT scores. Also, pre-registration (registration far in advance of the normal window.
(3) Lillian gave a poingnant assessment of the problems in Darfur--and how students can help this ongoing horrible problem
(4) Heather did a remarkable unusual report on civility--something very important to me--sensitivity to how people are treated. She discusses employing positive motivation to encourage civilitiy.
(5) Drew is focused on creating more school spirit during Little 500 by selecting a male and female student who embody the best at Indiana University. He has come to me during many off-hours to employ pert-chart techniques, for instance, to assess how to bring this to fruition.
(6) Tom gave a very unusual and controversal talk about global warming--and bravely (in my oppinion) sought to find the arguments to both sides of this attention-getting problem.
(7) Andy spoke about off-shoring and its positive effects.
(8) Morgan spoke on how to improve carpooling-especially in light of our connectedness in IT, but also brough a humanistic element. She proposed a very unsual system that I hope she suggests to UITS
(9) Logan spoke to a very practical, but difficult matter of certification--and employed several techniques in arriving at his solution. It is apparent he had been ruminating on this for some time.
(10) Kym spoke about how difficult it is for an honors student to pick classes without knowing what the student's intended major is--something she believes a number of honors students feel they need help with.
(11) Wesley addressed the controversial issue of raising minimum wage ant its effects on the different socio-ecomonomic aspects of our country.
(12) Linwood spoke about the pros and cons of legalizing marijuana, and provided the class with a number of fascinating statistics from the department of health, and many other governmental studies.
(13) Kurt addressed the frustration of registration as well--he, separately, arrived at a solution much like Charlie's, but also pointed out the latency between the number of actual open slots to slots shown through onecourse.
Some unsolicited comments (excerpts from emails w/ names removed) from studuents:
(I) Here is my final paper and powerpoint presentation. I hope you have a great break!!! I really enjoyed the class and you're one of the best professors I've had.
(II) I also wanted to thank you for the pizza on the last day and most of all for a great semester. I really enjoyed your class, and if my brother does come here next year I will try to get him into one of you classes (I will guarantee it if you can get some scholarship money sent his way : P). But seriously, you were an awesome professor and I wish you the best of luck in all of your endeavors. I will be sure to stay in touch, have a good break and rest of the year!
(III) I truly enjoyed your class first semester. As a freshman, it was nice to go to a class where the teacher cared more about the students and how much we learned than how much we could memorize. Even more than that I appreciated your help outside of class with in class, and outside of class projects. I hope you have a great break and I will see you when I get back with plans for our last project and an idea for a new one. Thanks again for everything.
The I519 had mixed results. It demonstrates to me the need for a separate track for biologists who want some dexterity with bioinformatics tools, but who don't want to be programmers. I was impressed with the number of simply outstanding MS students this year too.
I have finally submitted grades for both classes and am working on an ISMB paper.
Our football team is going to the Insight Bowl. Tickets are free to students--I hope we have enough folks attending. We beat UK in basketball, and my father called to suggest it might be good that his UT (Texas) team lose to MSU so IU would be ranked higher than UT. Nice.
- (edited December 16, 2007, 1:45 PM)
Scott and I attended the Seniors of IU Contemporary Dance Program on Sunday produced wholly by the students at the John Waldron Arts Center.
Bioinformatics meeting Friday--I still have emails to send out on topics.
Spoke with Andy--he's doing great and his wife is working on her MBA
Demonstrated CATPA added functionality for structure
Meet for School P&T (every Tuesday)
Visited IUPUI with Keith and Yaoqi to discuss curriculum. Met with the MD/PhD group Simon, Wade, and Maureen for the same. It was fun watching the students prepare for a histo exam--brought back some memories.
Drove home for Thanksgiving and drove back the same day ~ 8.5 hours, but absolutely worth it.
I guess ATT outsources their "you're over due buy a buck" people. I'm guessing the caller hails from somewhere near the Bay of Bengal. The issue I have (and I don't like to complain) is that I now have to pay two different ATT bills from the same website, each separately through two different accounts that have the same stupid information (stupid is duplication). Once I break my parents of their fax addiction, I'm moving completely to wireless like the saner people of the world. - (edited December 3, 2007, 3:52 PM)
Meet with P&T committee and inadvertantly missed meeting with candidate
Spoke with Jim, Jeff on Indigene and ISMB
Exchanged information with Luis about spring classes--must speak with the group - 1:06 AM
Today was I519 working on Markov Processes. I have notes I'll be providing.
Meet [with] Indigene group Jim, John, Brian, Justen, and Jeff examining data. I have been working through Gaussian Graphical Models.
Friday I was @ IUPUI to meet with Keith and Yaoqi working on curriculum. I then met with Simon, Maureen, and Wade discussing the potential collaborations and creating a better pipeline for MD/PhD students from Bloomington. It was a little strange for me, sitting outside of a lab exam as the medical students prepared. I don't remember it sounding that easy--age I guess. But they seemed to be having an excellent time. I *do* remember that.
I met with Jag from UMich and have promised him a paper on a quantified model of disease (first pass) that I co-authored with Pedja, Jim, and Wyatt.
I am meeting P&T tomorrow and am asked for a small task. I am on the Music Informatics Hiring Committee.
- 10:01 PM
Meet [with] Academic Council
Schedule trip to Microsoft eScience
Talk at Life Science Initiative sponsored by Kelley
I519 Homework 7 you'll find on oncourse too. - 2:49 AM
In H101 learned about structured reasoning.
Met with Bioinformatics group.
Here is H101 homework one
Met with Claudia and Jeff for Geology project.
Met with Scott. - 1:26 AM
Meet with Bioinformatics Group
Meet with Brent
Meet with Jeff
Meet with Jim
Trip to Texas (to check things out--and lucky enough to have tickets to the UT vs TCU game. Colt did great the second half--as did the linebackers.
Honors class is great.
Curriculum Strategic Committee.
Solution to I519 Quiz and another... Solution to I519 Quiz - (edited September 13, 2007, 12:24 AM)
Monday Panel II Meet the incoming students
Tuesday Meet [with] Bioinformatics Group. We introduced the core faculty Sun, Haixu, Pedja, Yuzhen, Matt, and me. We advised too--though we felt this year's advising was too different from what we've done before--so next year, we're going to the previous way.
Wednesday-Friday [with] Scott to discuss a pilot study for a portion of an EHR for the State of Georgia.
Saturday Picnic--lots of people, food, and good cheer.
Sunday meet my honors group @ Briscoe--nice bunch of students--I hope to make some connections with a few. It was enjoyable. - (edited August 28, 2007, 12:37 AM)
I generally don't do this, but I received a wonderful email from a student (whom I won't name) and it touched me greatly. Here it is:
Memo,
I never got the chance to really thank you for all you have done for me. You are the best teacher I have ever had and you are the reason, the inspiration I have, to continue in the field of Informatics. I know that if I had received another teacher other than you for the I101, I probably would not have been as enthusiastic as I am about the major. I tell everyone this, that you are the only teacher I have ever had that seems to actually care that their students learn the material and wants them to become something great. I imagine that most teachers have this passion for teaching, for making a difference in people's lives, when they first begin down that road. Sadly, I can see that most of them lose that passion in a short while. I can honestly say that you are one of those teachers who have retained that fervor for teaching and it shows. I am grateful that you have been offered tenure here at IU because now I know that not only myself, but others will have the benefit of having such an excellent teacher as you to inspire them. I don't know what courses it is that you'll be teaching. I do know that I would take them wihout a moment's hesitation just because of the fact that you'd be teaching them. Once again, thank you. Thank you for the pictures, the scholarship, the advisory council, and most of all, thank you for being the teacher and human being that you are. I wish for nothing but the best for you.
Thank you, (Name withheld) - 3:57 PM
I am now this year's Life Science's Group Leader.
Speak [with] Jim, Justen about PPI and MA data for flybase.
Book room in Vienna at Hotel Mercure Josefshof Wien for VLDB and Workshop on Data mining in Bioinformatics. - 1:31 PM
Meet Indigene Group (Justen, Jim, Scott, and Jeff) Brian and John were traveling.
Send a time for Jade's Capstone.
Meet Dean @ 10am
- 11:20 PM
Meet Haixu, Yuzhen, Sun, Matt for discussion of Bioinformatics.
Meet Andrew and Yuzhen about CATPA.
Meet Scott about Indigene.
Meet Haixu, Yuzhen, Sun discuss Bioinformatics. - (edited August 14, 2007, 11:18 PM)
Work on Indigene.
Update Wiki.
If you're interested, here's what we have access to in terms of software from Microsoft MSDN Academic Alliance
Here's my teaching schedule:
- INFO-H 101 INTRO TO INFORMATICS, HONORS (4 CR)
- 28245 RSTR 02:30P-03:45P TR I 107
- Laboratory (LAB)
- 28246 RSTR 09:05A-09:55A F I 109
- INFO-I 519 INTRODUCTION TO BIOINFORMATICS (3 CR)
- 29853 10:10A-11:25A MW I 107
- Laboratory (LAB)
- 29854 10:10A-11:25A F I 109
- INFO-I 692 THESIS/PROJECT BIOINFORMATICS (1-6 CR)
- 18048 PERM 06:00P-08:00P R I 107
Write a merit letter for Lynne Crohn, an amazing staffer in CS who takes care of any Window's bug you encounter!
I've sent out 19 personal letters to the incoming graduate bioinformatics students--Marty suggested this would be a great start in establishing camaraderie.
Start review for PSB! - (edited August 7, 2007, 9:01 PM)
Meet potential PhD student to fund with Michael from Statistics.
Meet Pete to discuss move.
Meet Andrews-Dalkilic Group (Justen, John, Brian, Jim, Jeff, Rupali, Scott) made excellent progress on Indigene.
The next CGB Roundtable:
What: Sriram Raghuraman will present "Error model for 454 sequencing".
When: Wednesday, August 8, 2:30 pm
Where: Myers 209
Sriram is a grad. student from the school of informatics. Since the beginning of this summer, he's been working with Dr. Haixu Tang on improving assembly of the 454 sequence reads. - (edited August 7, 2007, 6:15 PM)
I was approached by a student who was working on a physics problem. I've solved the problem and written a solution here.
Here is an interesting paper on DNA motifs:
Patrik D'Haeseleer
Nat Biotech 24 (4), 423-5 (Apr 2006)
PMID: 16601727 [PubMed - indexed for MEDLINE]
Here is the abstract: "Sequence motifs are becoming increasingly important in the analysis of gene regulation. How do we define sequence motifs, and why should we use sequence logos instead of consensus sequences to represent them? Do they have any relation with binding affinity? How do we search for new instances of a motif in this sea of DNA?"
We recently were accepted @ the GSA, Title: PRESERVATION AND DEVELOPMENT OF PALEONTOLOGY COLLECTIONS FOR RESEARCH AND EDUCATION Congratulations! This paper on which you are an author, has been accepted for presentation as indicated below. Your abstract will be published in GSA Abstracts with Programs Vol. 39, No. 6. The authors are Jeff R. Gehlhausen, Stephaney Puchalski, Claudia Johnson, Erika Elswick, David Polly, & Mehmet M. Dalkilic. The work. Here is the abstract of the full paper (tentative)
A growing debate about the fate of our planet has forced attention on ways to better understand how our planet's environment has evolved over the thousands of millenia. Informatics provides a means of gluing these pieces of evidence over the 4.6 billion years of existence. One approach is to examine an organism that has existed for a considerable amount of time and infer the environmental conditions during its existence. We approach this problem by creating a visualization and mining system for the organism chiton. Our project utilizes Microsoft's Virtual Earth as the main vehicle to visualize the organisms. - (edited August 5, 2007, 6:04 PM)
I received promotion and tenure and received the Trustee's teaching award. I am now also the Associate Director of Bioinformatics for Informatics (lots of Directors)
I've been moved back to the Informatics Building in my previous office--I have mixed feelings because all my colleagues are in Eigenmann.
We successfully hired Yuzhen Ye--a wonderfully gifted scientist!
I was invited to teach at IU's Mini-University--this is a weeklong event that alumni can retake special classes. 
Jim Shea, Director of the the Professional Development Programs, shared with my some of the comments form my session:
- IU, do not let him get away
- I almost dreaded coming into the session...what a pleasure surprise (the alum consequently told me she was apprehensive because of my name and my junior standing--but was so glad she took a chance)
- There were a lot of good sessions at this time, but I'm glad I picked this one
- The world is fundamentally different that it was an hour ago (That was a significant comment and outcome [Jim's comment])
Jim wrote to me that it was safe to say I wowed 'em and that I'd definitely be invited back to Mini! What a wonderful experience indeed. - (edited July 21, 2007, 12:39 AM)
Complete grading. MC for graduation dinner 06:00pm-09:00pm in Alumni Hall.
Monday
Meet for 3rd year tenure and provide materials for Dean.
Meet [with] Scott discuss Indigene
Tuesday
Begin teaching I201
Wednesday
Second day of class 201.
Meet [with] Justen - 8:45 PM
Meet [with] Chris for Capstone
Michael Trosset's Colloquium on classification.
Write-up for Graph algorithms from PhD students.
Add link to Probabilistic Methods for Active Learning and Data Integration in Computational Biology co-chaired by David Kreil and Peter Sykacek @ the University of Natural Resources and Applied Life Sciences, Vienna to the VLDB 2007 Datamining in Bioinformatics Workshop. David Kreil is co-chairing with Sun, Jiong, and me.
Become PC member of the 1st Workshop on Datamining in Uncertain Data (DUNE 2007) in conjunction with the 7th IEEE International Conference on Data Mining (ICDM 2007)
Attended Senior Capstone Fair. There were a number of great projects. I took a couple of pictures here. Charles Schneider and Eric Watson had me freshman year in I101. There project is Pipe-Line--bidding system for construction. 
Another project (with students whom I taught four years ago) was to add a mod to WOW--possibly one of the most enjoyable MMORPGs today (I'm a 70 Horde Shadow Priest).
Review PNAS paper with Justen and Jim.
Went to the Iron Pit.
Posted Summer Course I201 starting Tuesday May 8. - (edited May 1, 2007, 8:33 PM)
About 75 students and four faculty, Youn-Kyung, Erik, Sun, me and our great graduate student coordinator lead by Marty. We reflected on the year, had a complimentary repast of hotdogs (both normal and vegan) grilled primarily on one side by Richie. There was music and much rejoicing. I am posting a kind of panoramic picture of the circle with my LG 
On the right is Sun and to my left is Linda and Scott (I overheard Linda telling Scott not to look at me)
Monday
Meet [with] Andy about mining MS spectra.
Meet [with] Yin about Bioalgorithms class.
Meet [with] Hyejin about capstone.
Write letter for teaching for Ashley Williams in the Foster lab in Biology.
Respond to Amanda for I201.
Meet [with] Sun, Haixu, & Pedja for lunch and discuss sundry issues.
Tuesday
Meet [with] Sun, Haixu, Pedja, Matt for Jim and Amrita--PhD exam. The tentative schedule is 05/10/2007 10:00am..1:00pm, 2:00pm..5:00pm. Tentative 05/22/2007 10:00am..1:00pm, 2:00pm..5:00pm.
- (edited May 3, 2007, 5:57 PM)
Please visit http://www.alibris.com for out-of-print books. I found American Literature: a College Survey edited by Clarence and Flanagan, New York: McGraw-Hill, 1961. I was particularly looking for Tate's essays on Dickinson. - (edited April 22, 2007, 12:21 PM)
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