UNM Cyberinfrastructure Day 2010 presentation: Applications in Biocomputing, biomedical and cheminformatics research computing cyberinfrastructure issues.

1. Jeremy Yang
Software Systems Manager
Division of Biocomputing
Dept. of Biochemistry & Molecular Biology
UNM School of Medicine
Cyberinfrastructure Day -- April 22, 2010

2. I. What is Biocomputing?
II. Cyber Revolution (~1980-2010+)
III. Cyberinfrastructure (To be or not to be?)
IV. Super Computing, Redefined

3. Division of Biocomputing
http://biocomp.health.unm.edu/
Department of Biochemistry & Molecular Biology
School of Medicine
Also affiliated with the NIH Roadmap-funded UNM
Center for Molecular Discovery

4.  Biomolecular screening Data mining, machine
informatics learning
 Cheminformatics  3D visualization
 Bioinformatics  Public data integration
 Genomics  Collaborations in
 Virtual screening chemistry, biology,
medicine, comp sci
 Molecular modeling
 BIOMED 505 course
 SAR (Structure-
Activity-Relationship)  Software development,
management, deployment
& support

5. Larry Sklar, et al., UNMCMD (NIH Roadmap)
~$20M NIH awarded to date

6.  32 cpu Linux cluster  2+ Oracle instances
 32GB RAM server  PostgreSQL, MySQL
 Linux: OpenSUSE, CentOS,  Stereo graphics
RedHat, Fedora, Ubuntu workstation
 SGI/IRIX  25+ scientific software
 Windows, Mac OS X packages
 Automated integration with
 Supported in-house
NIH databases applications
We are cyberinfrastructure users and providers!

8. Virtual chemistry; property prediction, chemspace
navigation, computer aided molecular design, graph
theory, databases

9.  Nucleotide and protein sequence analysis
 Genomics, proteomics
 Merging with chemical biology, etc.

10.  Computational search for likely
biological actives Example:
3D shape search;
 Database may be real or virtual prozac & paxil
compounds
 2D and 3D methods
 2D similarity search
 3D similarity search (shape,
pharmacophore)
 docking (3D, protein binding site)
c/o OpenEye Rocs

11. atoms, bonds, surfaces, fields, interactions, stereo
serotonin
hemoglobin

12. Computational models for protein-ligand binding
Abl kinase
(1iep.pdb)‫‏‬
interaction potentia
hydrophobic (green
hbond acceptors (r
Gleevec in binding site
Gleevec is a leukemia drug known to bind with Abl kinase.

13. (Watch movies...)
PyMol movie:
http://video.google.com/videoplay?
docid=-5859274887925224981#
Jmol interactive DNA modeling demo:
http://chemapps.stolaf.edu/pe/protexpl/htm/top.htm?
id=1d66&&&chpa=true
Expert users can advance understanding via rich, dynamic, visual interfaces.

14. E.g., Searching NIH PubChem for non-selectivity

15. Many biomedical data sources worldwide
SLIDE 15 (15 MIN?)

16. Division of Biocomputing in 2008

17.  Rapid change, challenge and opportunity
 Learning from history, trends (new not enough)
 Winners and losers
 Science, experts have led and followed.
 ~1980-2010 covers 3σ (99.7%)
 And evolution...

18.  Rapid change, challenge and opportunity
 Learning from history, trends
 Winners and losers
 Science, experts have led and followed.
 ~1980-2010 covers 3σ (99.7%)
 And evolution...

19. 1977: Atari 2600
1978: Space Invaders
1981: IBM-PC (MS-DOS)
1983: cellphone
1983: GNU Project
1984: Neuromancer,
William Gibson,
“cyberspace”
1984: Apple Mac, mouse,
windows & icons

20. 1985: Oracle 5 (client-server)
1989: Intel 486 Pentium (1M
transistors, 50MHz)
1990: MS Windows 3.0
1990: WWW (Berners-Lee)
1991: High Perf Comp &
Comm Act (Al Gore)
1991: Linux (Linux Torvalds)
1991: AOL
1991: ETrade

21. 1993: Jurassic Park (via SGI)
1993: NCSA Mosaic
1994: Netscape Navigator
1994: “Good Times” hoax
1994: Match.com
1995: “Concept” virus (Word)
1995: Internet Explorer
1995: Apache project
1995: Yahoo!

22. 1995: Amazon.com
1995: My mother gets email
1997: Google
1997: eBay
1999: Melissa virus (Outlook)
1999: Napster (p2p)
2000: MS convicted
2000: 3M USA broadband*
2000: dot-com bubble pops
*Fixed non dial-up internet connections >56k (FCC).

23. 2000: 802.11b wireless
2001: Apple iPod
2001: Apple iTunes
2001: Wikipedia
2003: Skype
2005: YouTube
2005: Rio power grid hacked
2005: NSA domestic surveillance
2006: Facebook

24. 2006: Amazon Cloud
2007: DOD hacked
2008: 70M USA broadband*
2009: Cyberdefense USA priority
2009: Twitter role in Iran election
protests
2010: UAVs are SOPs
2011: Cyber terrorism?
*Fixed non dial-up internet connections >56k (FCC).

25. The dotted line keeps moving...
Case study: database cheminformatics in
pharma research, 1990→2000.

26.  In 1990, high speed chemical searching was
beyond standard capabilities.
 Research groups managed local servers in
their labs & specialized DB engines (e.g.
Daylight Inc.).
 By 2000, this function had moved to IT (via
Oracle cartridges, etc.) corporate informatics
infrastructure
 Transition not smooth, but very beneficial.

27. Standard cocaine
functions:
substructure,
similarity,
identity
chemical
searching
imidazoles

28. (1) office equipment
(2) lab equipment
(3) experimental apparatus
(4) the experiment
(5) a commodity
(6) custom configured experimental
vehicle for exploration
(5) all of the above

29. (1) office equipment
(2) lab equipment
(3) experimental apparatus
(4) the experiment
(5) a commodity
(6) custom configured experimental
vehicle for exploration
(5) all of the above

30.  Scientific software
 Computational science
 Commodity software
 Engineering enables science
 Science requires agile
development, high performance,
experimentation, risk taking,
play.
 Cyberinfrastructure users and
developers/maintainers
SLIDE 30 (30 MIN?)

31.  Scientific research  Scientific software for
experts
 Computational research
 Enabling software for
 High performance
scientists
computing as a research
tool  Commoditization (e.g.
cloud computing)
 High performance
infrastructure as a  Plumbing vs.
productivity tool experimental apparatus
 Appropriate tiers and
domains

32. IT: “Poorly managed Research: “We need
computers and needy ill- power, flexibility and
trained users put the access and not another
system at risk.” lame PC.”

33. And with other cyberfolks too. And with great
results.

34.  In ~5 yrs, super → un-super
 Super computing? Define computer.
 Advances from unexpected places:
 gaming, movies (graphics -- vs. AI)
 social networking (crowdsourcing)
 even business (web standards, UIs, security)
 Super computing is pushing the current limits
 But where are the key frontiers?

35. Advances from unexpected places...

36. Colossus code breaking computer, UK.

37. Eniac computer, Univ of Pennsylvania.

38. Cray computer

40. SLIDE 40 (40 MIN?)

42. High performance (super) computing is pushing the current limits.

46. This is what a “computer” looks like.

48. “The network is the computer.” - John Gage (Sun, NetDay founder)

49. Corollaries:
 The network is the (semantic) database
 The network is cyberspace
 The network is us too

50.  Super users → super computing
 Blackbox AI/monolith paradigm limiting
 Human/computer co-evolution
Cytoscape
biological network
visualizer with
drug - target
interactions

52. “Super Computers” @ Division of Biocomputing
 Tudor Oprea
 Cristian Bologa
 Stephen Mathias
 Oleg Ursu
Happy Earth Day!
 Jerome Abear
 Ramona Curpan
 Liliana Halip
Jeremy Yang
 Andrei Leitao jjyang@salud.unm.edu
Cyberinfrastructure Day -- April 22, 2010