Evolution of BINF Bioinformatics 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 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 Networking Data Storage Data Mining Grid Computing Storage Area Networks

Bioinformatics Technologies Informatics IT / Networking Molecular Biology Data Modeling Computational Biology Genomic Databases