BIOI 7711 Introduction to Bioinformatics

1
Welcome to Rocky 1
2
Go to the Mountains and Get their Good Tidings
John Muir

• Inspirations
• Adrenaline
• Beauty
• Life

3
Inspiration for a Revolution!

• Science is in the midst of a tremendous explosion
  of knowledge regarding of life
• Exponentially growing knowledge challenges
  humanitys ability to integrate and appreciate it
• Our era cries out for big ideas

4
A timeline and some great minds of biology
5
Why Rosalind Franklin?

• Womens enormous contributions to the study of
  life have often been downplayed
• Before she died of cancer at age 37, she produced
  the first X-ray crystal structure of DNA
• Watson and Crick were shown this image shortly
  before they produced their double-helix model
• Data drives modeling

6
The challenge of exponentially growing knowledge

• Numbers are articles from a given year.
• Fits an exponential curve with a 4.32 growth
  rateR2 0.998

7
Life is deeply connectedHigh order interactions
dominate

• Unsuspected connections in the last 3 years
• Uber-oncogene P53 plays an important role in
  aging
• Expression array studies of remodeling cardiac
  tissue after heart failure implicate role for
  genes well studied in pregnancy and embryological
  development
• Panadol, a drug developed for cardiovascular
  illness turn out to be very important in the
  treatment of depression.
• Gene-gene (or protein-protein) interactions are
  not pairwise, but very high order (often gt10)

8
Towards The Biological Knowledge-base

• Inferential potential of a unified knowledge-base
  transcends human ability
• Even heroic bioscientists cant keep up with
  flood of information as disciplinary boundaries
  break down.
• Computational integration efforts
• SOAP, GRID and especially the Semantic Web
• Beyond integration
• Knowledge dissemination timing and
  comprehensibility
• Making a compelling story from disparate bits of
  evidence

9
Biognostic MachinesAn AI Vision for
Bioinformatics

• From the Greek??????(life) and????????(knowing)
• The integration of humanitys knowledge of life
  in a computational system that can interact with
  bioscientists as a knowledgeable colleague
• Keeps up with the literature
• Can provide explanations and evidence for its
  statements
• Transcends disciplinary and terminological
  boundaries
• AI to the rescue?

10
A bit of AI

• Cognitive systems are driven by goals
• Experience, knowledge, memory, practice,
  learning, etc. inform both perception and action
• Sense perception provides incomplete and
  error-prone information about the world
• Action is organized and controlled to achieve
  goals (perhaps opportunistically)
• Mind is many distinct processes working together

11
Biognostic AI

• Goals
• Improve human health, diagnose and treat disease
• Pharmaceuticals their design and improvement
• Causal generalizations, understanding
• Experience (knowledge, memory, etc.)
• Up-to-date fact/knowledge-base, from textbooks,
  domain experts, journal articles, other databases
• Library of physical, statistical logical models
  and classes of models
• Sets of models parameters for particular
  applications

12
Biognostic Sensation

• Sensation is the use of pattern recognition
  (statistics) and knowledge to recognize
  opportunities for achieving goals via perceptions
  
• Biognostic Perceptions
• The biomedical literature (via information
  extraction)
• Databases GO/A, GenBank, expression databases,
  etc.
• Sense vocabulary GO, UMLS, NCI common data
  elements, ESV vocabulary, MAGE-ML, etc.
• Instruments? MS, NMR, etc. (or better from
  databases?)

13
Biognostic Actions Abilities

• Extract information from the literature
• Select models, fit parameters from data
• Learning, optimization, model competition
• Simulation / Prediction
• Application of models to unobserved circumstances
• Creation of new classifications or
  categorizations
• Communicating
• Explain, justify, answer questions,
  visualize/diagram
• Design experiments monitor or control
  instruments?

14
Vision versus Speculation

• Vision is necessary for engineering the tools to
  achieve it. Speculation is ungrounded and a
  distraction from doing the work
• Sometimes hard to tell the difference
• Biognostic machines may be vision, since
• Many pieces starting to fall into place
  Ontology, information extraction, semantic web,
  etc. etc.
• We are not alone Paul Allens Project Halo

15
Guide to next few days

• Purpose of the meeting is to build community
• Get to know each others names, work,
  institutions
• Find common interests and potential
  collaborations
• Let your hair down, have big ideas, have fun!
• Afternoons are part of the program
• Informal interactions are just as important as
  talks
• Good skiers find Elvis Marylin shrines (Back
  of Bell)
• Novices create a small group (4-8) for a joint
  lesson.
• Enjoy the town its easily walkable.

16
Thanks!

• International Society for Computational Biology
  Stephanie Hagstrom
• CU Center for Computational Biology Stephen
  Billups
• IBM (for dinner!), Kirk Jordan, Alex Zekulin, and
  the rest
• Apple and the other sponsors