Evolution of BINF Bioinformatics Certificate Foothill College R

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 Bio. Perl 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 Java. Script 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?

I 2 I Model • Synergy of technologies • Must be 25 years mature • Adapted from Technographics

Internet Technologies ini n g tin Da pu m Co ta M id Gr g CPU Data Storage Networking Storage Area Networks

Bioinformatics Technologies y g lo io Da ta M l. B na tio ta pu m od eli n Co g Informatics Molecular Biology IT / Networking Genomic Databases