Will be going to boston!! Enjoy my white-christmas with Fori , Chaitu and K-bhai. Pictures to come And well what all is boston about? Click here
Posts
Showing posts from December, 2003
- Get link
- Other Apps
http://www.cs.hmc.edu/qref/changevar.html#bash on Environmental Variables
HMC Homepage CS Home
* What is an environment variable?
* Some examples of environment variables
* Why do I want to change it?
* How to change environment variables:
o in csh/tsch
o in bash
o in other shells
What is an environment variable?
Environment variables set defaults for your shell to use to make life easier. They store data like which directory to look in for your home directory, which text editor you prefer, or which directories to check when running programs. If you didn't have your path environment variable set, you would have to run /usr/local/bin/programname or /usr/sbin/programname or whichever directory the program is in followed by its name, rather than simply typing in the name of the program you want to run.
You can find out what your environment variables are in csh/tcsh by running setenv. In bash you should run e
- Get link
- Other Apps
Viterbi Conference.
Talk by Michael Yaffee on Proteomic analysis of kinase signalling networks
- proteomic approach. how the information flows between the proteins.
- functionaly annotate proteome
- unify cell signaling and netw bilogy with bioinformatics
- identify druggable targets.
- - facilitate molecular analysis of chemical mechanisms
- provide a basis for understanding mutations.
- ctc2 kinase. Master regulator for cell division
- prevents the cells from dividing.
- we have a hierarchical process for phosphorylation and binding
domains.
- If we find motifs of the proteins .
Predict kinase substrates and binding domain.
pssm based on motifs from peptide libraryand phage display
experiments.
walk through the entire protein sequence db and score how good itis.
- Lets you make the call
- If the site were conserved.
Limitations:
1) Motifs based on peptides
2) pssms assume motif positions linearly independent.
- You can have pattern matchine
-
- Get link
- Other Apps
Have you taken BISC505 at USC. This might be helpful for final's preparation.
Mike's Section.
1) Sequence Assembly
History: When was DNA helix discovered. 1953.
When was the first free living orgranism sequenced.
When was the human sequence announced.
What is shotgun sequencing.
Facts about repeats in HG sequence.
Why was the hg sequencing difficult.
What were some of the innovations
Look at the exercise and midterm question.
There are many relevant databases. Be able to name a few databases.
Multiple Choices (can be expected).
Tim Chens: Around 3 questions , 1 for each.
2) Gene Finding, Proteomics and Genomics circuit.
1) Gene Finding:
Overview of the gene structures, prokaryotes and eukaryotes. Methods of gene finding (content of the methods). Score the signals
2) Proteomics:
a) Mass spectometry, lots of times. Exercise whether this is spectrum generated by the peptides. Applications of MS. Y2H , Gene knockout.
Pros an
- Get link
- Other Apps
A Nice talk on software innovations for CMB
Robert Gentleman - Harvard Biostatistics-
One of the pioneers of R and Bioconductor.
Software Innovation for computational biology and bioinformatics
- range of problems
methods for sequences,microarray,interactions,modelling,machine learning,
- Famous architect.
- More famous yesterday and today and more tomorrow and the day next.
- I am completely confounded by the idea of software reuse.
- To promote reproducible research.
ot hard.
1) Reduce complexity. Make life easy
2) Should provide basis of simulation.
3) Language sfor describing models.
AI NOT EQUAL TO i
COMPONENET SOFTWARE
1) SHOULD HAVE A CLEAR FUNCTION
2) A well defined set of inputs and ops
3) should be versioned
4) should have unit testing
5) should be automatically available
6) should be self documenting
- R Packages satisfy most of thest requirements.
- It is quite clear well defined web services can play a similar role. Given
- Get link
- Other Apps
Zope.org - What Is Zope? : "What Can Zope Do For You?
Zope can help you create dynamic web applications such as portal and intranet sites quickly. Zope comes with everything you need including support for membership, search, and news.
It's easy to use tools allow teams to productively and safely work together. Zope provides top-notch access to databases and other legacy data. Zope's open support for web standards such as XML-RPC, DOM, and WebDAV allows you unparalleled flexibility and interoperability.
On top of what Zope offers out of the box, there are useful applications available for those who need something right away:
The CMF (Content Management Framework) adds numerous tools and services to Zope to allow community or organization based content management, complete with a workflow system and a powerful customization framework. The CMF Workflow system uses Zope's built in security architecture. One thing this allows is for the 'edit permission' to b
- Get link
- Other Apps
Zope.org - What Is Zope? : "What is Zope?
Zope is an open source web application server primarily written in the Python programming language. It features a transactional object database which can store not only content and custom data, but also dynamic HTML templates, scripts, a search engine, and relational database (RDBMS) connections and code. It features a strong through-the-web development model, allowing you to update your web site from anywhere in the world. To allow for this, Zope also features a tightly integrated security model. Built around the concept of 'safe delegation of control', Zope's security architecture also allows you to turn control over parts of a web site to other organizations or individuals. The transactional model applies not only to Zope's object database, but to many relational database connectors as well, allowing for strong data integrity. This transaction model happens automatically, ensuring that all data is successfully stored in