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)

Workshop Satisfaction Data

Preliminary Student Learning Data

Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 Q19 Q200

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Pre-Course Post-Course

Prop

ortio

n of

Cor

rect

Res

pons

es

**

**

**

**

** ** **

*

**

**

***

**

*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/

ISCB Education Comm. - Curriculum Task ForceImplementation and refinement

• Partnerships– African Task Force on Bioinformatics Education

– University of Florida Bioinformatics Education Programs

– Ohio University Bioinformatics Education Programs

– NSF RCN?