Post on 27-Dec-2015
Professional Development
Anne Rosenwald, Georgetown University Vince Buonaccorsi, Juniata College
Linnea Fletcher, Austin Community CollegeBill Pearson, University of Virginia
Lonnie Welch, Ohio UniversityRobin Wright, University of MInnesota
• Teach faculty how to use basic web-based tools for bioinformatics• Make use of the data sources in the Human
Microbiome Project (HMP)• Create a community of practice for faculty and
their students on the companion website• http://genomesolver.org
• Collaborators: Gaurav Arora (GU), Jenna Canfield (Simmons), Mark LeBlanc (Wheaton), Ramana Madupu (JCVI), Janet Russell (GU)
Preliminary Student Learning Data
Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 Q19 Q200
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0.9
1
Pre-Course Post-Course
Prop
ortio
n of
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rect
Res
pons
es
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*p<0.05, **p<0.01
Next Steps
• Summer 2014 Workshops – MD and CA • IUSE grant pending – Convert current workshop to online format • Online Learning Initiative
– Expand the Community of Practice• Develop additional curriculum modules
– Horizontal Gene Transfer Project
Genes Shared by Bacteriophages and Their Hosts: PRIP in Chlamydophila pneumoniae and Chlamydia Phage
Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
Lonnie WelchDirector of the Bioinformatics Laboratory
Coordinator of Bioinformatics Certificate ProgramsStuckey Professor of Electrical Engineering & Computer Science
Biomedical Engineering ProgramMolecular & Cellular Biology Program
Ohio University welch@ohio.edu
Curriculum Task Force (CHAIR)Education Committee (VICE CHAIR)
International Society for Computational Biology (DIRECTOR)
International Society for Computational Biology:Computational Biology Spanning the Globe
• Over 3,000 Members
• Scientific Leaders and Research Professionals, Postdoctoral Fellows, and Students
• Nurtures communities that consider important topics in computational biology
Africa
Asia
Australia and Oceania
Europe
North America
South America
ISCB Membership by Region
+ The ISCB Education Committee Curriculum Task Force
Welch LR, Schwartz R, Lewitter F.
“A Report of the Curriculum Task Force of the ISCB Education Committee.”
PLoS Comput Biol. 2012 Jun; 8(6):e1002570.
programming/scripting/software engineering
statistics/probability
databases
cellular and molecular biology_x000d_
algorithm design/data structures/computation theory
machine learning
genomics
basic biology
evolutionary biology
molecular genetics/population genetics
mathematics
phlyogenetics
sequence analysis
bioinformatics tools
biochemistry
data/text mining
next generation sequencing
protein structure and function
network and pathway analysis
proteomics
sequence alignment
structural biology
systems biology
comparative genomics
information systems/data management
ontologies
computer networking
homology modelling
microarray
0 5 10 15 20 25 30 35 40
Biology,Chemistry
Computation,Math, stats
+
Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, et al. (2014)
PLoS Comput Biol; 10(3): e1003496.
Approach
• Survey of Core Facility Directors
• Survey of Career Opportunities
• Survey of Existing Curricula
• Synthesis of core competencies
Types of Bioinformatics Training
• Bioinformatics users
• Bioinformatics scientists
• Bioinformatics engineers
BioinformaticsUser
Bioinformatics Scientist
Bioinformatics Engineer
An ability to use current techniques, skills, and tools necessary for computational biology practice.
X X
X
An ability to apply mathematical foundations, algorithmic principles, and computer science theory in the modeling and design of computer-based systems in a way that demonstrates comprehension of the tradeoffs involved in design choices.
X
ISCB Education Comm. - Curriculum Task ForceImplementation and Refinement
• Cycle 1:– July 2014: presentation and discussion at ISMB– 2014-2015 academic year: implementation– July 2015: presentation and discussion at ISMB– August 2015: draft report– Fall 2015: publish report
• Cycle 2: 2015-2016 academic year
• Cycle 3: 2016-2017 academic year
ISCB Education Comm. - Curriculum Task ForceDissemination
• Presentation and discussion at ISMB – the largest computational biology & bioinformatics conference
(~1500 attendees!)https://www.iscb.org/ismb2014
• Publish reports in the ISCB Society pages of PLOS Computational Biology Journal
(More than 9000 article views in the first 5 weeks!)http://www.ploscompbiol.org/