Associate Professor Informatics @ Indiana University, Bloomington- Graduate Programs Director
- Andrews-Dalkilic Laboratory @ Dept. Biology Indiana University, Blooomington
- Associate Director Bioinformatics @ Indiana University, Bloomington
- Associate Center for Genomics and Bioinformatics
- Adjunct Assistant Professor Computer Science
- AGEP Faculty
- H101, TR, 2:30-3:45pm, I107, F lab 9:00am-10:00am
- I519, WM, 10:10am-11:15am, I107, F lab 10:00am-11:00am
- Capstone, typically R at 7:00pm
- WM, 12:00pm-6:00pm, Myers
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
Handed back Exam I in H101
Creating revisions for homework--this weekend.
Worked on P & T
Got Altas Shrugged, The Stranger, Pride and Prejudice, In the President's Secret Service: Behind the Scenes with Agents in the Line of Fire and the Presidents They Protect, The Lost Symbol books for students, and various music too, Brahms, Prokofiev, Mozart, Gregorian Chants; sheet music (Suites from Debussy)
While at one of the entrances of Hell (I was able to shoot two pictures before the forces of evil disabled my phone) The rolodex to the right are the souls of produce.
I was accosted by a young man who found a young praying mantis (the color and texture of grayish tree bark), distressed what to do. I promptly offered to take the mantis to somewhere safe.
and placed him in one of the trees on the west side of Kroger. Bloomington is "Tree USA", after all.
I also watched nearly half a dozen brave souls, of a larger contingent, creating The School of Informatics and Computing - Bloomington, Bloomington, Indiana's float 
.
This is homecoming week--and although I like the weather, it's not conducive to crepe paper.
I must show Kan's disdain for my having to do work at home--the laptop is at the left. 
I will eventually show what he does inbetween these misleading cute, passive poses. The last thing to say is that I must be a luddite.
The last image is of my television informing me I should pay my bill...my television...What happens when the house is eventually tethered electronically, and your electric toothbrush flashes, "Pay the TV--and buy more Crest?" I'm glad I've kept the clock I had in high school--no electronic soul or enough silicon to give messages other than static or an annoying beep to rouse me from sleep. I know it's probably paranoid, but I could swear the television was trying to turn-off the other electrical devices in the room until I looked at it squarely and performed what is asked.
Meet Miles.
Let's hope for a blowout in the Red River Shoot Out. I'm looking for Colt and Shipley to have a great game, dispensing with OU. 
- (edited October 16, 2009, 5:20 PM)
It was a closer game than I would have liked, but Texas beat Colorado handily in the third and fourth quarters. For any who watched the game, Shipley and the great defense was the answer. Completed grading H101 Exam and gave an exciting homework III.
Ordered books and more music for Honors students.
Odious, necessary errands today too. I am looking forward to my new website. - (edited October 16, 2009, 4:11 PM)
Our Drosophila paper in Genome Biology has been accessed 1938 times so far and is now designated in Genome Biology as "highly accessed". Please visit Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
Beginning the onslaught of P&T cases.
Attended Life Sciences Reception Faculty/Employers/Students Wednesday, October 7th, 7:00 p.m., President’s Room- Indiana Memorial Union. - 4:56 PM
Scott and I and the gym--a the story of...well, he's very sore today LOL. His text to me is "I so ***** sore" which sums it up.
Meet Justen, Bobak and get Indigene.org back-up (Owe Dave cookies)
Group working on similar things: Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics
Jim is good
Bought Terbyte Drive for Jim's data
Kan is up to date with shots. Our vet Alice at Bloomington Vet. Hosp. was great. Alice surely must be one of the best vets in the world!
Tuesday lunched with A. The food was actually healthy AND good--she has always had exquisite taste!
Own Jayce mock-up still needed
Post Homework and class notes and finish exam grading. - (edited October 6, 2009, 5:33 PM)
Faculty Nomination
Addressing Internet Problem
UG committee
Discussed the undeniable wisdom of banning flavored cigarettes with students. I find this decision so sublime, that listening to Magnificat in D, BWV 243 Quia Respexit...Omnes Generationes
is the only means I have to fully comprehend not only the law, but also the great minds that were intrepid enough to identify and stamp out this problem. I do have an admittedly silly thought: will flavored cigarettes become among the ilk of guns, heroin, extortion...trafficking of cookie dough cigarettes. We must be vigilant.
Let's hope there's a kind of cosmic hiccup, and we beat the OSU tomorrow. So a mystery has occurred. I embarrassingly spend too much on books, mostly at Amazon and even have the Kindle DX. So the mystery--yes. After ordering 16 copies of a book for my honors class, the order, according to UPS via Amazon had shown the delivery was made two weeks prior--Sept. 16. There was a green colored bar, which I guess indicates successfully delivered. Oddly, I had not received the books. I contacted Amazon and explained about the nearly identical addresses in my planned housing division, and the likelihood the books were no more. Amazon contacted UPS, then responded to me that UPS ackowledged deliverying the books to the wrong address. True to Amazon's wonderful service, it sent me an additional 16 books at no charge overnight. Herein lies the mystery. UPS delivered what appears to be the original order that night, then the duplicate order the day after. Amazon did not send three orders of 16 books (I've just spoken to them). How could UPS have delivered the books, yet ostensively deliver the same order to me weeks later? Hmm.
Just finished reading Lies! Lies!! Lies!!! The Psychology of Deceit. It's interesing, though somewhat dated, account of lies through the lens of a psychiatric physician. I encourage reading of the book, if for no other reason than to dispel widely held mythoi of affectation, ability to detect lying, and so forth.
One of my I101 students is now graduating. William Falotico is an amazing student, and from what I've seen, just as an amazing employee. Please visit his website to read more about this young man who came to me as an enthusiastic 18 yo and is going to the Kelley soon. - (edited October 2, 2009, 2:44 PM)
Meet with Andrew
Meeting for Division C P&T (from 3:00pm until somewhere near 9:00pm)--in I105 no less.
Meet at Hutton Honor's College (Sunday)
Meet with Hutton Honor's College (Private)
Write letter of nomination.
Meet with Scott
I've finished The First Word: The Search for the Origins of Language. It's more of a survey, but informative; there is a decent mix of philosophy, biology, and speculation. Like "Nutureshock" I have to post notes later. I will post my first exam which included readings from by MacFarlane, The Information Paradox by Thorp, and Doubt by Hect. These may be a strange trio--and they are. MacFarlane's book as a fascinating social network of accusations. It bares an eerie similarity to Facebook (in its connections). Thorp's book discusses the apparent dogma that technology improves situations, but somehow the improvement is elusive to quantify or even formally recognize. This is particular true with IT. Hecht's book offers a "doubters" quiz. I was interested in seeing where on the scale they stand. We'll see tomorrow.
Meet with Chris
I'll be doing the accounting for my class and the Lotus Festival. I paid for the ticket, if a student attended. My order of 16 books, The Man Who Mistook His Wife for a Hat was delivered to another address--similar to mine. Unfortunately, the resident disposed of the books somehow (I'm thinking burning, but using them for the small, loud dog--think birdcage--is another alternative). I'm contacting various state and federal agencies to see if this somewhat mean-spirited reproach is actionable. I hope it is--not the least of which is because I'd like my items back LOL. I presume the resident is unfamiliar with any technology post 1960--so, this blog will be unread. - 3:58 PM
Jim and Lisa have graduated and now reside on the east coast in a beautiful--but haunted--house. Our paper--really the core of Jim's work--Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function in Genome Biology. The work is the first integration of genome-wide experimental data for fly. Jim's post-doc'ing at Collin's lab studying sythetic and systems biology. Lisa's at Brown doing her post-doc. Moving Jim's furniture with DL, Scott, Brian (and eventually...eventually Richie and his new sidekick) was a study in how a collectin of Type A personalities that run the gamut of OCD, which needs to be treated because it's so severe (Scott had to take calming breaths as we stacked boxes) to OCD, which needs to be treated because it's so severed (I wanted to understand why anyone would move cardboardesque furniture). BTW, a shoutout and apology to Jim's mother. I didn't know it was a gift, but in my defense, Jim couldn't explain what it actually was.
My 2nd year honors class is a blast. I'll be posting images and URLs from them too. There was even a waiting list to get in LOL. Unfortunately, like Charlie: they are locked in. Props to Nick for wearing Harry Potter's cloak LOL.
Kan's brother passed away two months ago. Oakley was a remarkable canine--wildly tempermental, mischievious, and loving. Kan and I both miss him. Kan's doing very well--our last daily walk he tried to bring down a deer. He's feral; I don't care what anyone has to say.
Justen and I are continuing Jim's work--and I have a number of projects ongoing. Being on the P&T committee eats up a lot of time--but it's important--especially in light of the changes this year at IU.
The Lotus Festival is this week. I can't say for sure, but it seems a couple of the flowers I worked on a couple of years ago are floating amongst the pages LOL. I did graphics anonymously for Lotus as succor for someone who, as it turns out, is really an insect. Now, with a priori help from me, which I solemnly regret, it (the afore mentioned insect) has managed to burrrow its way into a medical school and infest other people. I had thought an email (what I know now as a disingenuous response to an initial email from me about a graduation) was nothing more than mimicking friendly, human communication. Okay--it's what insects do, right? Or don't do--no disrespect to people who own "pet" roaches. But my gut tells me, the roaches would be in the same (lack of) state of mind, rollining crap in the wild as they would be housed in a cup (rolling in crap). In the end, being an insect is its own unawares punishment. One fewer bug in Bloomington. octies novem: sit omni genere laborum fatigatue exorit.
Today we review the three cases of our division...Division C. I don't know why it's C. I'm a faculty fellow for Briscoe--we need to set a time to all meet. NP hard for sure. I've given Josh a code so his "association" (of 250 people) (which I doubt) and all watch Sunny in Philoflorida or some such.
I just finished reading Nuture Shock by Bronson and Merryman. Not very technical, but an excellent collection (compiled by the authors) of recent work by scientists on cognitive research of growing-up. Much of the mythos of raising and dealing with the young and young adults are directly studied--and some provocative (at least for now) results have begun to emerge. As I write this, I wonder about the results had the scientists studied insects too? I've finished three others this week--but time, the devourer calls me thither. I'll look for the books' images--makes it so much more palatable when recommending them.
- (edited September 25, 2009, 2:56 PM)
- (edited October 10, 2008, 11:02 PM)
Full faculty meeting on structure
Meet with Geoffrey on Graduate Programs
Meet with Claudia, Simon, Geoffrey
Email Dean of George Washington Medical School
Kan comes back from the vet--I pray he'll be ok.
Working on biological validation for paper in Justen's lab.
Working on calling GPC initial meeting.
If you like great music I recommend Reneé Fleming, Handel Arias
- (edited September 18, 2008, 2:12 PM)
Orientation Week went well. I am the new Graduate Programs Director--and my mission is to help students and advisors achieve the productivity and education possible. I am working on examining how to allow other units to take credited hours within Informatics. I introduced myself three or four times--we'll see if the students remrember me. As of yet, I do not have an AI for my Honors I101--which is a bit distressing--I hope for a good resolution. I just got my I519 AI.
I advised the first year MS students (whom I blame for my flu). I also helped with PhD students, but met with Geoffrey during the second year MS students.
Our Center for Bioinformatics Research Center has been just approved--so I'm eager to get started. Yu-Wei is back from China, but need to see Trent and Michael. Jim's marriage was a wonderful event and I was honored to be among the few who were at both the ceremony and reception. Linda, a close friend, bet me a dark chocolate bar about someone not attending--she was right, but to much chagrin. It was great to see Andy who brough green tea. So I'm set for a month or so. I believe the days I will be in Biology will be TWR.
I will contact Justen and Jim on this. I have finished the H101 and I519 courses (to the left) and have remaining the capstone.
I'm eager to resume my quantitative modeling of disease and working with Dirk at MeadJohnson. I am also completing parts of a data mining book glycomics with Haixu and Yehia. I am working on finishing my I101 text before it goes into oblivion. I miss Bill a lot. I do still sometimes thing about my insect friend too.
I finished the book The Man who Mistook his Wife for a Hat
The interesting thing is this chronicles lesions in the right brain--which hasn't been studied nearly as much as the left hemisphere.
- (edited September 18, 2008, 2:13 PM)
Neal-Marshall Black Cultural Center
275 N. Jordan Avenue
(Corner of 7th and Jordan)
3:30pm-4:00pm Director of Graduate Programs
The full schedule
- (edited September 1, 2008, 9:17 AM)
Worked in Jordan with Jim and Justen on Indigene--I'm running MEME on Big Red--lots of motifs
Working on expression data and another paper on disease
- 2:29 PM
I also spoke at IU's mini-university on the Electronic Alaphabet--sort of a primer for grandparents. With my student Jim and colleague Justen we've finished the first iteration of indigene and is under submission. I'm excited that I have an opportunity to work with Milton Taylor in our Biology Dept. and will be submitting a grant with Geology on acidification of parts of the gulf. I'm slated to teach honors I101 and I519 again in the fall--and we'll see what else.
I've finished reading 
Mother Theresa: Come Be My Light. I'm going to present passages from the books I read--for amusement, maybe edification--who knows. I hesitated to start with this book, lest folks conjecture I'm overly religious--she lead a fascinating life and it's worth reading.
- (edited September 18, 2008, 12:29 PM)
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)
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