1. Computational Biology Trends and Careers www.flickr.com

2. Introduction Olena 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

3. Talk Outline What is Computational Biology? Current Trends and Challenges Careers Q/A http://www.sciencedaily.com/images/2005/07/050730093601.jpg

4. 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

5. Computational Biology is... http://compbio.cs.huji.ac.il/

6. Research Directions Dynamical Interactions Structures and Functions of BioComponents Design of Artificial Components

7. Dynamical phenomena in cell Del Castillo & Moore, 1959

8. Networks and Relationships of Biological Components W.Chen & B. Schoeberl, 2009

9. 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/

10. Producing and Utilizing the Knowledge www.biomedcentral.com/.../1471-2105-6-287-1.JPEG

11. 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

12. 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

13. Talk Outline What is Computational Biology? Current Trends and Challenges Careers Q/A http://www.sciencedaily.com/images/2005/07/050730093601.jpg

14. Current Trends and Challenges Overall trend: More people are recognizing that computer science can enable biological discovery Prof. Stephanie Taylor, Colby College

16. Grand Challenge: Relating genotype to phenotype in complex environments (iPG2P) Genotype The exact DNA sequence of an individual Phenotype The collection of all observable and measurable traits of that individual (Zhang et al. BMC Plant Biology 2008)(Wood et al. Science, 2001)

17. iPG2P: Multi-scale, Dynamic Problem (ghr.nlm.nih.org; wikitextbook.co.uk; generalhorticulture.tamu.edu; scienceblogs.com)

18. 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

19. 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.

20. 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.

21. 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.

22. Talk Outline What is Computational Biology? Current Trends and Challenges Careers Q/A http://www.sciencedaily.com/images/2005/07/050730093601.jpg

23. Careers in CompBio Manasi 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

24. 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

25. 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.

26. 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

27. 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

28. 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!

29. 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

30. +/- ProsCons Very hot field, professionals in demand Industries wary of investing too much Universities hiringNot 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 applicationsSkepticism about the field

31. 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/