Evolution of BINF Bioinformatics Certificate Foothill College R. Cormia, L. English, K. Erickson.
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Transcript of Evolution of BINF Bioinformatics Certificate Foothill College R. Cormia, L. English, K. Erickson.
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