Educational Activities in Cheminformatics at IU

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Jan 31, 2013 (4 years and 4 months ago)

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Educational Activities in
Cheminformatics at IU

Gary Wiggins

wiggins@indiana.edu

Overview


Enrollment data


Newer educational activities


Formal courses


Degree programs

Enrollment Data in the Period
of the NIH Grant


Currently have 4 PhD students, 2 MS, 1 BS


96 students have taken at least one
cheminformatics course since August 2005


29 of them (30 percent) accessed the
courses through distance education means


17 DE students in I571



9 CIC CourseShare students in I571



2 DE students in I572



1 DE student in I573

Breakdown by Courses


Enrollment by Courses,

(August 2005


present,
across both campuses)

I/C371

9

I/C372

14

I533

6

I571

44

I572

12

I573

5

I590

2

I647

4

TOTAL

96

Newer Educational Activities


Graduate Certificate in Chemical Informatics


Cheminformatics Resources Web Guide


Ongoing Work with Mesa Analytics on the
Cheminformatics Virtual Classroom


Drug Discovery Database at IUPUI


Development of Formal Courses

Graduate Certificate in Chemical
Informatics


Requirements: 4 courses; each 3 cr. hours


I571 Chemical Information Technology


I572 Computational Chemistry and
Molecular Modeling


I573 Programming for Science Informatics


I553 Independent Study in Chemical
Informatics


Available to on
-
site IUB/IUPUI and Distance
Education students

Cheminformatics Resources
Web Guide


http://www.chembiogrid.org/related/index.html



Academic Programs


Chemistry Databases on the Web


Professional Societies and Groups


Companies and Independent Institutions


Publications and Conferences


Data Standards and Standards Groups


Molecular Visualization Tools and Sites


Web Services Technology Resources


Other Guides to Cheminformatics Resources

Training Modules for Chemical
Informatics Instruction


Mesa Analytics Cheminformatics Virtual
Classroom


http://www.chemvc.com/


BCCE (Biennial Conference on Chemical
Education) workshop on cheminformatics, July
30, 2006



Creating a Distributed Drug
Discovery Database

o
Enumeration software is used to create large sets of
potential product molecules.

o
A list of potential drug lead candidates is split into small
batches for synthesis in academic laboratories
throughout the world.

o
The pooled molecular products are tested by a
distributed screening effort.

o
The sum of these efforts becomes a powerful globally
distributed drug lead process and solution.


DDD keeps track of data

o
Features

o
Entry of reagents in the database

o
Generation of combinatorial products

o
Entry of synthesized products information

o

Release:

o
Web application to enable data entry/searching of
DDD database

o
Workflow environment to support pipelining of tasks
involving DDD database

o
Web services to facilitate integration with other
resources (e.g., PubChem)


Database Built on:

o
PostgreSQL

o
Java and HTML user interfaces

o
Tomcat Server and JDBC driver

o
Chemaxon

o
Marvin Sketch

o
Marvin View

o
JChem Reactor

o
http://cheminfo.informatics.indiana.edu:8080/
ddd/first.html


Entity
-
Relationship Diagram


Student Participation in DDD

o
The synthetic laboratory experimental work is
done in these locations around the world:

o
Indianapolis

o
Barcelona

o
Moscow

o
Lublin.

o
IUPUI C444 Organic Chemistry Laboratory

o
Summer 2006: 33 students

o
Fall 2006: 20? students


Formal Courses


Undergraduate courses


I371 Chemical Informatics (1 cr. hour)


I372 Molecular Modeling (2 cr. hours)


Introductory graduate courses


I571 Chemical Information Technology


I572 Computational Chemistry and Molecular Modeling


I573 Programming for Science Informatics


I617 Informatics in Life Sciences and Chemistry (core PhD
course for non
-
majors)


Seminars, etc.


I590 Information Retrieval from Chemistry and Life Sciences
Databases (Topics Course)


I533 Chemical Informatics Seminar


I647/I657 Advanced Chemical Informatics Seminar I
-
II

Cheminformatics Seminar


I533 Seminar in Chemical Informatics


Spring 2006 Topic: Molecular Informatics, the
Data Grid, and an Introduction to eScience


http://www.indiana.edu/~cheminfo/I533/533home.html


Six students enrolled

I647 & I657 Advanced Chemical
Informatics Seminars I
-
II


Topics vary yearly and include:


representation of chemical compounds


representation of chemical reactions


chemical data, databases and data sources


searching chemical structures


calculation of physical and chemical data (molecular mechanics
and quantum mechanics)


calculation of structure descriptors


methods for chemical data analysis


integration of cheminformatics and bioinformatics


Fall 2006 topic: Bridging Bioinformatics and Chemical
Informatics


http://www.indiana.edu/~cheminfo/I647/647home.html


4 students enrolled


Degree Programs: BS and MS


BS degree


34 credit hours of Informatics courses


Cognate area, usually a minor in areas such as chemistry,
biology, computer science, fine arts, business, etc.


MS degree: 36 semester hours


Includes a 6
-
hour capstone/research project


IUB: Bioinformatics, Chemical Informatics, Human
-
Computer Interaction


IUPUI: also, New Media, Health Informatics, Laboratory
Informatics


Unique MS Program at IUPUI


Laboratory Informatics at IUPUI


Instrumentation and data interfacing


Laboratory notebooks


Laboratory Information Management Systems
(LIMS)

Degree Program: PhD in
Informatics


Began in August 2005


The 90 hours of credit for the PhD in Informatics
(cheminformatics track) consist of:


27 hours of required informatics courses


I501 Introduction to Informatics (3 cr.)


Core informatics courses (9 cr.)


Seminars in the cheminformatics track (6 cr.)


Professionalism/Pedagogy course (3 cr.)


Research Rotations (6 cr.)


12 hours in theory or methodology courses (or credits from an
MS degree)


21 hours of electives (or credits from an MS degree)


30 hours of dissertation research.


Concentration Areas for the
PhD in Informatics


Tracks:


Bioinformatics


Chemical informatics


Health informatics


Human
-
computer interaction


Social and organizational informatics


Under development:


Complex systems, networks, modeling and simulation


Security


Music informatics


New media

END

Software/DBs Used in the
Program

Company




Products and/or (Target Area)

ArrgusLab



(Molecular modeling)

Digital Chemistry (formerly, BCI)

Toolkit (Clustering)

Cambridge Cryst Data Center


Cambridge Structrual DB & GOLD

CambridgeSoft



ChemDraw Ultra

Chemical Abstracts Service


SciFinder Scholar

Chemaxon



Marvin (and other software)

Daylight Chemical Info System

Toolkit

FIZ Karlsruhe



Inorganic Crystal Structure DB

IO
-
Informatics



Sentient

MDLCrossFire



Beilstein and Gmelin

OpenEye




Toolkit (and other software)

Sage Informatics



ChemTK

Serena Software



PCmodel

Spotfire




DecisionSite

STN International



STN Express with Discover (Anal Ed)

Wavefunction



Spartan

Core and Affiliated Faculty


MU
-
HYUN BAIK


KELSEY FORSYTHE


GEOFFREY C. FOX


SANTIAGO SCHNELL


DAVID J. WILD


DIMITRIS AGRAFIOTIS
(adjunct)



JOHN M. BARNARD
(adjunct)


DONALD B. BOYD

(affiliated)


ROBERT D. CLARK

(adjunct)


DAVID E. CLEMMER

(adjunct)


CHARLES H. DAVIS

(affiliated)


THOMPSON N. DOMAN

(adjunct)


KEVIN E. GILBERT

(affiliated)


GARY M. HIEFTJE

(adjunct)


JOHN C. HUFFMAN

(adjunct)


PETER J. ORTOLEVA
(adjunct)


GARY D. WIGGINS

(adjunct)


FAMING ZHANG

(affiliated)

Outreach Activities


Research relationships with


IU School of Medicine


IUB/IUPUI bioinformatics and proteomics
research programs


Commercial firms through internships
(LeadScope, Rosetta Inpharmatics, Lilly, etc.)



Why IU for Chemical Informatics?


Outstanding Faculty


Excellent computer facilities and infrastructure


Close proximity to major pharmaceutical companies
(Lilly, Abbott, Pfizer) and to chemical informatics
companies (Tripos, LeadScope, Chemical Abstracts
Service)


History of innovative, IT
-
based chemical information
services (QCPE, MSC)


Complementary programs in IU’s School of Library
and Information Science (SLIS)

Introducing Graduate Students
to Cheminformatics Research


I571, I572, and seminar projects


Research rotations of PhD students


RA assignments