User:Boris

Boris Steipe  (course coordinator)

Medical Sciences Building, Room 5368

Toronto, Ontario      M5S 1A8

T: 416-946-7741

E: boris.steipe@utoronto.ca

Extension and Template syntax

... under development

• User:Boris/Temp/APB - Applied Bioinformatics page hierarchy
• User:Boris/Temp/BIO - Bioinformatics page hierarchy

• User:Boris/Temp

• Cargo Cult Bioinformatics
• VMD tutorial(s)
• R tutorial
• Stereo Vision tutorial

Assignments

Assignment_DEV_1	Assignment_DEV_5	Assignment_DEV_9
Assignment_DEV_2	Assignment_DEV_6	Assignment_DEV_10
Assignment_DEV_3	Assignment_DEV_7	Assignment_DEV_11
Assignment_DEV_4	Assignment_DEV_8	Assignment_DEV_12

Page templates

• Multi Boiler Plate extension drop down menu

(Copy Template location from there to edit.)

 

Original sidebar links

• Main_Page
• BCH441Hwiki:Community_portal
• Current_events
• Special:RecentChanges
• Special:Random
• Help:Contents

• What links here ... try ctrl- option - j
• Related Changes ... try ctrl- option - k
• Special:Upload
• Special:SpecialPages

Quick resources

• MediaWiki:Common.css
• MediaWiki:Sidebar

Additional BIO Topics

• Must make note to alert students who run LINUX boxes that some assignment tasks can be conveniently Perlified.
• http://www.biosolveit.de/PoseView/

Additional CSB Topics

http://www.elsevier.com/wps/find/bookdescription.cws_home/707460/description

• Elsevier - Introducing Computational Systems Biology
• Elsevier - Enabling Information and Integration Technologies for Systems Biology:
  • Elsevier - Databases for Systems Biology.
  • Elsevier - Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology
  • Elsevier - Integrated Imaging Informatics
  • Elsevier - Simpathica: A Computational Systems Biology Tool within the Valis Bioinformatics Environment
  • Elsevier - Standards, Platforms and Applications
• Elsevier - Foundations of Biochemical Network Analysis and Modeling
  • Elsevier - Introduction to Computational Models of Biochemical Reaction Networks
  • Elsevier - Biological Foundations of Signal Transduction and the Systems Biology Perspective
  • Elsevier - Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis
  • Elsevier - Integrated Regulatory and Metabolic Models
• Elsevier - Computer Simulations of Dynamic Networks
  • Elsevier - A Discrete Approach to Network Modeling
  • Elsevier - Gene Networks: Estimation, Modeling and Simulation
  • Elsevier - Computational models for circadian rhythms: Deterministic versus stochastic approaches
• Elsevier - Multi-Scale Representations of Cells and Emerging Phenotypes
  • Elsevier - Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks
  • Elsevier - Spatio-Temporal Systems Biology
  • Elsevier - Cytomics—from cell states to predictive medicine
  • Elsevier - The IUPS Physiome Project: Progress and Plans.

Additional APB Topics

• • GPU and Cloud computing
  • CSS ( http://www.csszengarden.com/ , http://en.wikipedia.org/wiki/Help:User_style , )
  • REST as API. Programming example: SADI or BOLD (Barcode of life).
  • GO annotation in http and R

Bioinformatics

	Biological foundations	Data	Analysis	Interpretation
Sequences
Structures
Evolution
Systems

Utilities

This is the path to the pmid document repository to provide direct links to PDF's for loged in users. Every user needs to have this section in their User page, the Template:pubmed uses the userfunctions, parserfunctions, and lst extensions to pull the section pdf_repository_path from a user's page and construct a link to the repository. Naturally, this works only for pmid's for now.

biochemistry.utoronto.ca/steipe/abc/376CEB52AF96EA94