Educational &Community Extending

Activities

Education Outline

Graduate training/mentoring Undergraduate training/mentoring Courses with Biogeometry Community education Participation in new initiatives

Education of new scientists

Senior Research Associates – Robert Gdanitz NCAT Physics– Patrice Koehl Stanford Biology

Postdoctoral Fellows – David Hsu UNC CS– Michael Prisant Duke Biochemistry– Jeffrey Roach UNC Biochemistry– Farbian Schwarzer Stanford CS– Alper Üngör Duke CS– Afra Zomorodian Stanford CS – *Lutz Kettner MPI Saarbrucken– *Robert-Paul Berretty Philips Research– *Nayana Vaval NCAT Physics– *Sergei Bespamyatnikh U Texas Dallas CS

Education of new scientists

Graduate Students

Serkan Apaydin Stanford EEAndrew Ban Duke BiochemDeepak Bandopadhyay UNC CSHamish Carr UBC CSAbhijit Guria Duke CSMartin Isenburg UNC CSRachel Kolodny Stanford CSAndrew Leaver-Fay UNCCSLoren Looger Duke BiochemItay Lotan Stanford CSAndrea Mantler UNC CSAjith Mascarenhas UNC CSNabil Mustafa Duke CSVijay Natarajan Duke CSAn Nguyen Stanford Sci CompDavid O'Brien UNC CS

Sean Palmer UNC BiochemDaniel Russell Stanford CSJaewon Shin Stanford EE*Rohit Singh Stanford CSChris Varma Stanford CSYusu Wang Duke CSKevin Wedderburn NCAT Physics *Afra Zomorodian Stanford CS *Anne Collins Duke Math*Zaki Abdulrahman NCAT Physics*Cecelia Procopiuc Duke CS*Amit Singh Stanford Biochem

Rohit Singh, finding motifs in proteins, best Stanford CS MSc thesis, June ’02

Education of new scientists

Undergraduate Students– *Eric Berger Stanford CS– Patrick Chan Duke CS– Julie Greenberg Harvard  – *Emily Humphrey UNC CS– *Shilpa Khatri UNC Mathematics– Lekisha Perry NCAT Physics– *McKenzie-Marie Slaughter Hampton CS– Sewyalew Taddele NCAT Physics– *Smriti Bhotika UNC CS

Courses – at all university levels

New courses– CPS 296.1 - Bio-Geometric Modeling: course

notes online to become monograph (Edelsbrunner)  

– Algorithmic Biology (Batzoglu, Guibas, Latombe)– Comp006d – Folding: from paper to proteins:

Freshman seminar (Snoeyink)

Courses – at all university levels

Biocomputation lectures in existing classes:– CS326 – motion planning: molecular motion, probabilistic

roadmaps, self-collision detection (Latombe)– CS468 – intro to computational topology: finding pockets

and tunnels in molecules, compute surface areas and volumes and their derivative (Guibas; Zomorodian)

– SB228 Protein Simulation and Structure Prediction (Levitt)– Comp205 – scientific & geometric computation: protein

representation, molecular dynamics (Snoeyink)– Comp016 – Intro to scientific programming: reading and

processing PDB format files (Snoeyink)– Bioc134 – Molecules (Carter)

Workshops

Thus far, annual meetings have been for project team and invited guests

To broaden this meeting, we've organized the

2002 Triangle Biophysics Symposium, Friday & Saturday

Hoped for 80, but have nearly 100 attending

DIMACS & NSF Motion Workshops (Agarwal & Guibas)

New initiatives

NC A&T GAANN grant for Interdisciplinary Training in Biotechnology, Genomics and Bioinformatics.

NC A&T Sloan foundation feasibility study for MSc in Computational Sciences

UNC Bio-informatics training program – Research rotations, e.g.

• Crystal Wright, UNC BMME (Snoeyink; CS)• Andrew Leaver-Fay UNC CS (Tropsha; Med. Chem.)

Stanford BioX program – Levitt & Latombe server on the leadership council

Duke PhD program in Bioinformatics and Genome Technology.– 2 core CS courses: Algorithms in Comp. Bio. & Bio-Geometry

Other community involvement

UNC Program in Cellular and Molecular Biophysics (Carter, Snoeyink)

Stanford Graduate Curriculum Committee, Bio-Engineering Dept., (Latombe)

Hiring of new faculty (e.g., at UNC, Dokholyan, Kulmann, & Wang)

Visitors (e.g. at Stanford: Prof. Ileana Streinu, Smith College, 6 months, from Sept.’02)

Conference participation, organization, program committees, …

Other

On-line – Biogeometry web pages– Biocomputing Notebook, Tutorials, etc

Monograph on Bio-Geometric Modelling (Edelsbrunner)

Software

Under-represented groups

Represented in all of the above– Initiatives at NC A&T– Selection of undergrad researchers, rotation

students, visitors

COMP 6: Folding from paper to proteins

First year seminar – Origami– Robot manipulator motion– Protein Folding