Evolution of BINFBioinformatics Certificate

Foothill College

R. Cormia, L. English, K. Erickson

BINF - Bioinformatics

• A 60 unit certificate– 65% biology– 35% CIS– 10% math

• Targeted at returning adults– “dot.com refugees”– Biologists with vision

Deploy, Manage, and Evolve

• A strategy framework– Using metrics to manage strategy – Effective in business analysis

• Deploy a certificate

• Manage for “best fit”

• Evolve for continued success

Reasons to Write a Certificate

• Because you can

• Because it looks good

• Because it makes sense– We “think” it will benefit students– But it needs real planning and management

• Good gardens don’t just happen

Certificate Deployed

• Responding to a perceived need

• Built a certificate “off the shelf”– A little, bio, a little CIS, a little math

• We put together an advisory board

• By chance we have an instructor or two with both CIS and biology experience

Then We Blended

• Everything we had

• Molecular biology

• DNA sequencing

• PERL programming

• And a course in statistics– Pretty much everything we had– “Off the shelf” components

Retrofit vs. Introfit

• Working with 30 to 50 yr. Adults– Many dot.com refugees with bio exp.– Adding bio or CIS to complement skills– Adding career life to experienced adults

• Working with Gen Y– Building for a homogeneous future– Biology, informatics, and CIS are seamless

So What Was That Problem?

• Oh yeah, too much data, and no underlying understanding of biology

• What was going to be useful to our graduating students?

• Teach only what’s needed short-term?• What about using computers to model and

solving biological problems?• How do we blend biology, CIS, and math?

What Not to Do?

• Well – let’s not create courses that solve biological problems (hmm..)

• We can start by teaching straight CIS

• And maybe teach biology without informatics (hmm..)

• And then we’ll teach statistics without biological problems as applications

Half Hearted Efforts

• Sequencing with some BLAST

• XML with some BSML

• Perl with some BioPerl modules

• Less than 10% of our certificate is designed explicitly for bioinformatics

• Are we creating any new courses to model and solve biological problems?

Math Informatics (1)

• Basic probability

• Description of statistics

• Hypothesis testing

• Linear algebra, matrices and vectors

• Hidden Markov Models (HMM)

MINF – Math Informatics (2)

• Metrics and Similarity Measures • Dynamic Programming• Hidden Markov Models • Information Theory: Entropy and Mutual

Information

• Advanced Topics (Overview):– Neural Networks– Classifiers and Clusters– Primary Component Analysis

Suggestions for Managing

• Encourage faculty advisors for students within our certificates

• Integrate problem based learning into our courses

• Develop learning around questions

• Bring in more professionals as students

• Try to partner with other institutions

Courses Without Differentiation

• Unix

• Perl

• SQL

• Oracle

• JavaScript

• HTML

• Statistics

Evolving - Breaking the Mold

• Take 5 unit CIS courses to 3 + 2 units

• 3 units lecture

• 2 units lab / modules– Need to find “off the shelf” labs– Problem based learning and applications

• Can collaboration helps us evolve?

Lab Components that Model Biological Problems

• Probably what we need most

• CIS needs “domain applications”

• Students need “real world” problems early in their bio and CIS coursework

• Interaction with other institutions

• Collaborative problem solving

Bioinformatics – Two Approaches

• The first approach– Biology and biotech– CIS and programming– Mathematics / informatics

• The second approach– The problem domain– The data domain– The analysis domain

• What if we taught bioinformatics as a practice?

Evolved - Following the Industry

• Genomics

• Proteomics

• Physiomics– Vs.

• Biology

• Computer science

• Mathematics

Questions (1)

• What are the goals of our students?

• What are the needs of industry?

• Are classes designed around students?

• Or are students designed around classes?

• What about preparedness issues?

Questions (2)

• What was the goal of the certificate?• Selection issues for laboratories

– Torture vs. outcomes

• Do we really create integrated curriculum – or just classes?

• Making post transnational modifications to our certificate

• Intro-fitting vs. retro-fitting: what if the student(s) were the center of the universe?

Summary

• Not a bad start• We blended chocolate and vanilla• We really need bio-centered curriculum• How to help our CIS / math courses?• How to meet the needs of students?

– Initially we “retrofit”– Eventually we “introfit”– “Practice centered” students?

I2I Model

• Synergy of technologies

• Must be 25 years mature

• Adapted from Technographics

Internet Technologies

CPU

NetworkingData Storage

Dat

a M

inin

gG

rid Com

puting

Storage Area Networks

Bioinformatics Technologies

Informatics

IT / NetworkingMolecular Biology

Dat

a M

odel

ing

Com

putational Biology

Genomic Databases