Mehmet Dalkilic, PhD
September 24, 2006
Sunday
A flood of emails from L519 and I101--I101 is due at midnight.

L519 Lab II additional information. I have added some responses to oncourse through email you should receive soon. - (edited September 24, 2006, 6:36 PM)

September 22, 2006
Thursday-Friday
Thursday I101 Began speaking about loosely structured problem solving--establishing the correct problem statement is critical if a satisfactory solution is to be found.

At both 9:30am and 1:00pm classes Jeremy came to pitch the Future IT Potential gathering. There are no labs that week of Oct. 6--attending the fair is the lab.

Friday

10:30am-11:45am Indigene and strategy discussion

11:30 [with] Scott, Claudia, Erika--Microsoft Invited Abstract on Paleoinformatics

12:00pm-2:00pm Full Faculty meeting (CS+~CS)

3:00pm-3:30pm meet [with] Chris

2:00pm-4:20pm L519 Lab II Assignment due tentatively in three weeks--read conditions please.

4:40pm meet [with] Sun updates

5:30pm meet [with] Andy and Haixu on Chemistry project. - (edited September 22, 2006, 8:56 PM)

September 21, 2006
Tuesday--Wednesday
Tuesday I101 Truth tables, tautogolies, contradiction, and material implication. We also met Modus Ponens.

9:30am-10:15am and 1:00pm-2:15pm. Homework due Sunday at midnight.

Met [with] Nathan to discuss getting a MS in Bioinformatics--what's needed.

Met [with] Haixu and Andy on Chemical MS/Graph Association Rule Mining. Interpreting results and rules and interest in understanding the data distribution of peaks vs. graph elements.

Wednesday L519 Continue with BLAST, deriving lambda in our most famous equation E=kmne-λS - (edited September 21, 2006, 9:05 AM)

September 18, 2006
Monday
L519 Scoring Matrices and BLAST.

Meet [with] Scott about Indigene.

Justen Andrews talk at Myers Hall 4:00pm 103 on Indigene.

Please visit The Future Potential of IT for careers in the IT field hosted by The School of Informatics and The Kelley School of Business, Bloomington, IN.

Date: Friday, October 6, 2006.

Time: 12:00pm-2:15pm concluding with a drawing of an Xbox 360™

Where: Solarium (Next to Alumni Hall) - (edited September 19, 2006, 1:53 AM)

September 16, 2006
Wednesday - Friday
L519 Wednesday we discussed Smith-Waterman and extension to assignment on search space.

I attended the Employer's Panel then dinner with various Business representatives who will seek employees at the IT Fair.

I101 Thursday we continued with converting base 10 to an arbitrary base and discussed algorithms. We then constructed an algorithm by composing two smaller algorithms. We began doing Propositional Logic and Circuit Design too. I promised I would post homework tonight, but it will be tomorrow.

10:00am-12:00pm Friday Indigene group completed MetaCyte grant--Justen did the main authoring and we met to discuss IGERT talk on Wednesday.

12:00pm-2:00pm Faculty hiring

2:30-3:00 met [with] Andy about lab in L519--CGI for next laboratory assignment.

3:30 [with] Adrian about possible C# track

4:00-6:00pm Life Sciences group (some folks missing unavoidably) points for Geoffery to bring to the gathering of group leaders to Bradford woods.

- 1:20 AM

September 12, 2006
Tuesday
Taught I101 Continued with base conversion--then introduced Propositional Logic and Circuits.

Meet [with] Chris to discuss classes

Homework for I101 will be posted Friday.

- (edited September 12, 2006, 7:22 PM)

September 11, 2006
Monday
L519 discussed Smith-Waterman, PAM, BLOSUM. Began explaining about normalizing the raw scores in the matrices. Also discussed the terms "motif" "domain" "sequence motif" and "structural motif" and "consensus".

Submitted abstract to Microsoft's eScience Workshop 2006 with Claudia and Erika [both from Geological Sciences].

I encourage all students to attend the IT Career Fair September 14, 2006 @ 10:00am-3:00pm Alumni Hall.

And also the Employer Panels September 13 2006 @ 4:00pm Informatics Building.

For more careers check out www.iuinformaticscareers.com The fair has grown a lot in just three years!

2004 – 21 Employers

2005 – 42 Employers

2006 – 65+ employers projected - (edited September 12, 2006, 7:21 PM)

Monday - Sunday
Monday [in] L519 gave extension to first lab assignment and went through dynamic programming and Needlemen-Wunsch and global alignment.

Tuesday [in] I101 we continued with bases converting from one base to decimal.

Meet with and take notes for Undergraduate Committee @ 3:00pm-4:00pm. Posted notes on oncourse.

Wednesday [in] L519 went through Smith-Waterman alignment and gap penalties--discussed local alignment.

Thursday [in] I101 we continued with bases.

Friday meet [with] Andy and Haixu and discuss chemical database rule mining

Saturday meet [with] Jim and Jeff for Independent Study - 5:48 PM

September 3, 2006
Saturday & Sunday
Meet [with] Jeff and Jim for project

Meet [with] Scott

PSB Poster acceptance

Answer question from Michelle for L519 on requirements. - (edited September 3, 2006, 10:57 PM)

Friday
Indigene Meeting [with] Jim, Justen, John, Scott, and Brian--Scott demo'd Indigene visualizer in C#.

Faculty Meeting @ noon until 02:00pm.

L519 Lab is to get warmed-up and make students ask questions about practical issues. Andy Lin is the AI. - 10:19 PM

Thursday
Notes in preparation: In I101 we began discussing what it formally means to be a problem. We looked at a simple Turing Machine and figured out how it worked. We also discussed abstractly what problem solving is. We discussed structure adds: reproducibility, verifiability, and measurement. Labs began. LAB I includes among other things, how to find one's computer accounts at IU.

Spoke with several studentst then [with] Chris who doesn't like his picture taken. We had tea at Starbucks--he had questions about Informatics.

Life Sciences Meeting 04:00pm-05:00pm where we selected representation:

  • Geoffrey Fox, [Sun Kim] when Geoffrey cannot attend
  • 2 representatives per group for the Undergraduate Program Committee
    • Mehmet Dalkilic
    • Predrag Radivojac

  • 2 representatives per group for the Graduate Program Committee
    • Mookie Baik
    • Matthew Hahn

  • 3 representatives per group for the Graduate Admissions Committee
    • Mehmet Dalkilic
    • Haixu Tang
    • David Wild
    • [Geoffrey Fox]
    - (edited September 3, 2006, 10:27 PM)
Wednesday
Notes from L519 in Preparation--but basic topics included Central Dogma, Translation, Transcription, Proteins; We further discussed the differences between structured, semi-structured, and unstructured data. In particular what role does meta-data play and how biological data is different from generated business operational data. We discussed formats--and spent time on Fasta.

Lunch [with] Brian and Mark (Candidate for Campus Bioinformatics Director)

Evolutionary Computational Genomics/Bioinformatics
Faculty Recruit: Dr. Mark Batzer

Title: Mobile Elements and Primate Genomic

Variation @ Wednesday, 008/3006 4:00pm JH009

- (edited September 5, 2006, 2:58 PM)

Tuesday
I am teaching two sections of I101 this semester. More can be found at I101 Description

INFO-I 101 INTRODUCTION TO INFORMATICS (4CR)
CLSD 18248 01:00p-02:15P TR WY005 79 seats

Introduction to Informatics, problem solving skills, technology, thinking outside the box.

Laboratory

  • 18249 06:50P-07:40P R SE045 29 seats
  • 18250 09:05A-09:55A F ED2025 25 seats
  • 18251 01:25P-02:15P F HP154 29 seats

INFO-I 101 INTRODUCTION TO INFORMATICS (4CR)
CLSD 27005 09:30A-10:45A TR I107 38 seats

Introduction to Informatics, problem solving skills, technology, thinking outside the box.

Laboratory

  • CLSD 27006 05:45P-06:30P R SE045 12 seats
  • CLDS 27007 09:05A-09:55A F BU407 12 seats
  • CLSD 27008 10:10A-11:00A F BU407 12 seats

Lecture One We introduced ourselves. The syllabus was discussed, the expectations of the class, what the lab was like and Informatics in general. We also discussed "cognates"--the specialization within the degree.

Our first assignment was to get a 3x5 card, a picture of ourselves, with the following information: what would I be if I could be anything; my avocations; a secret nobody knows about me. The class link can be found on the right pane. - (edited September 3, 2006, 9:27 PM)

  • Phone: (812) 856-5754
  • Phone: (812) 856-3010
  • FAX: (812) 856-1995
  • Email:
  • Office 229
    901 East 10th Street
    Indiana University
    Bloomington, IN 47408-3912