Transcript Detailed PowerPoint of this Project

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
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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
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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)
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Basic probability
Description of statistics
Hypothesis testing
Linear algebra, matrices and vectors
Hidden Markov Models (HMM)
MINF – Math Informatics (2)
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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
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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)
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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
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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
Data Storage
Networking
Storage Area Networks
Bioinformatics Technologies
Informatics
Molecular Biology
IT / Networking
Genomic Databases