Computational Biology

Trends and Careers

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IntroductionOlena Marchenko, Senior, Colby College: Computer Science and Molecular Biology.

Manasi Vartak, Senior, Worcester Polytechnic Institute: Computer Science and Math.

Nancy Amato, Professor, Dept. of Computer Science and Engineering, Texas A&M University: Motion planning, computational biology, robotics, computational geometry, animation, EDI, VR. Parallel and distributed computing, parallel algorithms, performance modeling and optimization. amato@cse.tamu.edu

Anne Condon, Professor, Dept. of Computer Science, University of British Columbia: Computational complexity theory and design of algorithms, prediction of the secondary, structure of nucleic acids, design of molecules using prediction tools. condon@cs.ubc.ca

Stephanie Taylor, Clare Boothe Luce Assistant Professor, Dept. of Computer Science, Colby College: Systems Biology, phase sensitivity of oscillatory systems, computational models of circadian clocks. srtaylor@colby.edu

Special thanks to Prof. Raquell Holmes

Talk Outline

• What is Computational Biology?

• Current Trends and Challenges

• Careers

• Q/A

http://www.sciencedaily.com/images/2005/07/050730093601.jpg

What is Computational Biology?

Computational molecular biology is conceptualizing

biology in terms of molecules & applying

“informatics” techniques - derived from disciplines

such as mathematics, computer science, and statistics -

to organize and understand information associated

with these molecules, on a large scale

(Gerstein, 2007)

Olena Marchenko, Colby College

Computational Biology is...

http://compbio.cs.huji.ac.il/

Research Directions

• Dynamical Interactions

• Structures and Functions of BioComponents

• Design of Artificial Components

Dynamical phenomena in cell

Del Castillo & Moore, 1959

Networks and Relationships of Biological Components

W.Chen & B. Schoeberl, 2009

Data Types vs. Abstraction Level

•DNA/Amino acids

sequences

•Protein structure

•Intermolecular interactions:

•Dynamics of interactions

•Systems

http://www.bioteach.ubc.ca/what-is-bioinformatics/

Producing and Utilizing the Knowledge

www.biomedcentral.com/.../1471-2105-6-287-1.JPEG

Computational Approaches

Modeling regulatory networks

– Bayesian Networks

Inferring regulatory network models from

experimental data

– microarray data

– computation inference of module networks

Architectural properties of regulatory networks

– modular structure of regulatory networks

•Ask the right questions

•Select/Build the tools

•Learn more about the system and ask new questions

Ultimate goal : to understand all aspects of an

organism and its environment through the

combination of a variety of scientific fields.

Underlying Approach

Talk Outline

• What is Computational Biology?

• Current Trends and Challenges

• Careers

• Q/A

http://www.sciencedaily.com/images/2005/07/050730093601.jpg

Current Trends and Challenges

Overall trend: More people are recognizing that computer science can enable biological discovery

Prof. Stephanie Taylor, Colby College

Grand Challenge:Relating genotype to phenotype in complex environments (iPG2P)

GenotypeThe exact DNA sequence of an individual

PhenotypeThe collection of all observable and measurable traits of that individual

(Zhang et al. BMC Plant Biology 2008)(Wood et al. Science, 2001)

iPG2P:Multi-scale, Dynamic Problem

(ghr.nlm.nih.org; wikitextbook.co.uk; generalhorticulture.tamu.edu; scienceblogs.com)

iPG2P:Multi-scale, Dynamic Solutions

(ghr.nlm.nih.org; wikitextbook.co.uk; generalhorticulture.tamu.edu; scienceblogs.com)

Bioinformatics: learn from the data

Modeling: simulate the dynamical interactions among components

iPG2P:Cyber-infrastructure Challenges

Data management. Relating different data. Learning from the data.

1. Good middleware for virtual, integrated, distributed databases: Pipelining of NextGen sequence data into virtual genotype and molecular phenotype databases.

2. Data integration (adding depth and context to establish relationships and meaning) – relate information from such virtual databases to permit deeper insights, generation of hypotheses, evaluation of models, practical applications, etc

3. Statistically-based tools for use in inferring relationships. Many such tools exist, but the value-added aspect in the current context is to make them smoothly interoperable with the other features of the cyberinfrastructure.

iPG2P:Cyber-infrastructure Challenges

Data and model visualization.

4. Visual analysis tools. It is necessary to present integrated data to users in ways that are both concise and revealing. This includes multi-dimensional data displays.

iPG2P:Cyber-infrastructure Challenges

Modeling and model analysis.

5. Modeling framework tools to support the construction, parameter estimation, sensitivity analysis, and utilization of models. Again, the value added is in interoperablility.

Talk Outline

• What is Computational Biology?

• Current Trends and Challenges

• Careers

• Q/A

http://www.sciencedaily.com/images/2005/07/050730093601.jpg

Careers in CompBioManasi Vartak, Worcester Polytechnic Institute

• CompBio as an Undergrad• CompBio in Grad school• Jobs in CompBio

- Teaching- Research- Bio/Pharmaceutical Industry- Computer Industry

• What does it take? • Pros and Cons

CompBio as an Undergrad

• Not a mainstream major (Exceptions: U. of Nebraska, George Washington U. etc)

• Alternatives:– Concentration or focus– Bio + CS double major– Computational Science and Engineering major– Interdisciplinary courses: Bio, Math

department

• Summer Research Programs– CRA-W DREU, UConn Health Center

CompBio in Grad School I

• MS/Ph.D. programs at several universities– Harvard, MIT, CMU, Princeton, UW, ETH

Zurich, Cambridge University, EPFL, Max Planck Institute etc.

• Program administration:– CS programs with CompBio focus– Joint/Interdisciplinary programs – Programs administered by

Biochemistry/Bioengineering depts.

CompBio in Grad School II

• Specific funding opportunities:– Ph.D.: IGERT: Integrative Graduate Education

and Research Traineeship– Postdocs: NIH/universities/research labs– Traditional opportunities

• Part time option: – Grad courses at universities– Online courses

Jobs in CompBio I

• Teaching:– Faculty at a university: research + teaching– Hot area; universities looking for talent

• Research:– CompBio scientist:• Labs: National Research Council IIT

Bioinformatics Lab, Canada; IBM T. J. Watson Research Center• Medical centers: UConn Health Center

– Software engineer at research lab

Jobs in CompBio II

• Bio/Pharmaceutical companies:– Pharma CompBio divisions: Genentech,

Amgen etc.– CompBio companies: Zymeworks, Entelos

• Software Development Companies:– Write software for use by biologists e.g.

modeling, simulation, data mining– CS skills can land you a job anyway!

What does it take?

• Willingness to collaborate!

• OK with not knowing everything

• Understanding that not everything has a rigid algorithm

• Understanding the qualitative and quantitative aspects of the work

+/-Pros Cons

Very hot field, professionals in demand

Industries wary of investing too much

Universities hiring Not too many positions

Opportunities for making big contributions; few senior researchers

Success depends on collaborations; your part in the success may be small

Real life applications Skepticism about the field

Resources

• www.iscb.org *

• www.bioinformatics.org

• http://ocw.mit.edu/OcwWeb/Biology/7-91JSpring2004/CourseHome/

• http://stellar.mit.edu/S/course/6/fa08/6.047/

• http://www.embl-heidelberg.de/

• http://www.ncbi.nlm.nih.gov/pubmed/16650809

• http://iplantcollaborative.org/

• http://www.bioteach.ubc.ca/what-is-bioinformatics/

• http://www.cs.washington.edu/homes/tompa/papers/