Difference between revisions of "User:Boris"
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====... under development==== | ====... under development==== | ||
| + | |||
| + | ;CSB map | ||
| + | <table border="1"> | ||
| + | <th> | ||
| + | <td>00</td> | ||
| + | <td>prereading</td> | ||
| + | <td>topic</td> | ||
| + | <td>exercise</td> | ||
| + | </th> | ||
| + | |||
| + | <tr> | ||
| + | <td>01</td> | ||
| + | <td>-</td> | ||
| + | <td>Intro</td> | ||
| + | <td>Wiki</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>02</td> | ||
| + | <td>Annotation</td> | ||
| + | <td>Web</td> | ||
| + | <td>GO, GOSemSim</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>03</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Gene lists</td> | ||
| + | <td>FAA, GSEA</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>04</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Genome, transcriptome</td> | ||
| + | <td>GEO (4+5)</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>05</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Proteome, Metabolome</td> | ||
| + | <td>GEO 2?</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>06</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Graph theory</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>07</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Interactome</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>08</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Networks</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>09</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Systems extraction</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>10</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Dynamics</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>11</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Modelling</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>12</td> | ||
| + | <td>prereading</td> | ||
| + | <td>Synthetic biology</td> | ||
| + | <td>exercise</td> | ||
| + | </tr> | ||
| + | |||
| + | </table> | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
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* [[User:Boris/Temp/APB]] - '''Applied Bioinformatics page hierarchy''' | * [[User:Boris/Temp/APB]] - '''Applied Bioinformatics page hierarchy''' | ||
Revision as of 02:40, 23 January 2014
Boris Steipe (course coordinator)
- Medical Sciences Building, Room 5279
- Toronto, Ontario M5S 1A8
- T: 416-946-7741
- E: boris.steipe@utoronto.ca
Contents
... under development
- CSB map
| 00 | prereading | topic | exercise | |
| 01 | - | Intro | Wiki | |
| 02 | Annotation | Web | GO, GOSemSim | |
| 03 | prereading | Gene lists | FAA, GSEA | |
| 04 | prereading | Genome, transcriptome | GEO (4+5) | |
| 05 | prereading | Proteome, Metabolome | GEO 2? | |
| 06 | prereading | Graph theory | exercise | |
| 07 | prereading | Interactome | exercise | |
| 08 | prereading | Networks | exercise | |
| 09 | prereading | Systems extraction | exercise | |
| 10 | prereading | Dynamics | exercise | |
| 11 | prereading | Modelling | exercise | |
| 12 | prereading | Synthetic biology | exercise |
- User:Boris/Temp/APB - Applied Bioinformatics page hierarchy
- Cargo Cult Bioinformatics
- VMD tutorial(s)
- R tutorial
- Aminoacid tutorial
- Stereo Vision tutorial
- Database Identifiers
- Integrated_Exam_Questions
Page templates
(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
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
PediaPress mwlib mediaWiki → eBook extension/software.
