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Welcome to PlatcomWiki

Contents 1 Simple Rules 2 Lab 2.1 Our web servers 2.2 Lab Meeting (Microbial Projects) 2.3 On-line Lab Note 3 Share your programs 4 Share your tips 4.1 System Variables (PLATCOM, COMPATH, BIOALGO) 4.2 Comparative Genomics 4.3 Unix/Linux 4.4 Weka 5 Paper Links 5.1 Enzyme Classification 5.2 Enzyme Structure-Function Linkage 5.3 Genome Annotation 5.4 Metabolic Pathway 5.5 Gene Finding 6 External Links 7 Understanding MediaWiki

Simple Rules

PlatcomWiki is an web collaboration environment for Prof. Sun Kim's research group members. We will share our scripts, programs, modules/packages, and valuable tips via this wiki.

• Kwangmin will manage this wiki. If you need to create account, please contact kwchoi_at_indiana_edu
• Don't re-invent the wheel!
• Only registered users can read/write/edit wiki articles and only superuser can delete existing articles. Current user is Dr. Sun Kim, Ankita Bhan, Youngik Yang, and Kwangmin Choi (superuser).
• You need to use standarized input/output file formats.
• Creating orphan pages is not recommended. Whenever you create your artice, you should make at least one "internal" link to existing wiki page.
• You have to search our wiki database before creating a new article in order not to create the same (or similar) page again.
• Please use platcom@googlegroups.com to send out a note to all members.

Lab

Our web servers

• PlatCom
• ComPath
• CGAS

Lab Meeting (Microbial Projects)

• Lab Meeting 2008
• Genome Annotation Meeting 2008
• format for cluster representation

On-line Lab Note

• Kwangmin Choi

Share your programs

Please describe your program as in unix man page. You need to specify input/output file format in your description and provide sample input/output file if needed.

Categories are as follow (The list will be extended later.):

• Gene finding
• File search
• DB search
• Parsing
• Standard file format

A program can be included into your wiki article only if it is short. If not, please store your program in /var/www/html/platcom/wiki/programs/ directory Your sample input/output file need to be stored in /var/www/html/platcom/wiki/data/ directory.

Share your tips

System Variables (PLATCOM, COMPATH, BIOALGO)

• Read GLOBAL_VARS page to look up our system variables!

Comparative Genomics

• Image:Species tree.jpg

Unix/Linux

• wget

Weka

• command-line execution

Paper Links

Enzyme Classification

• Umar Syed & Golan Yona, Enzyme function prediction with interpretable models (In Computational Systems Biology, Humana Press. (R. Samudrala, J. McDermott, R. Bumgarner, Editors).

Enzyme Structure-Function Linkage

• Patricia Babbit, Definitions of enzyme function for the structural genomics era

Genome Annotation

• Troy Hawkins & Daisuke Kihara, Enhanced automated function prediction using distantly related sequences and contextual association by PFP

Metabolic Pathway

Gene Finding

External Links

Understanding MediaWiki

If you are new to wiki grammar, please visit the following links or visit wikipedia.

• Consult the User's Guide for information on using the wiki software.
• Configuration settings list
• MediaWiki FAQ
• MediaWiki release mailing list