CLCG Tutorials

This document is a working draft of several outlines of tutorials for both staff and students of the CLCG (Coordinated Laboratory for Computational Genetics and Genomics).

A. Filesystem structure
B. Accounts
C. Processes/Daemons
D. Environment Variables
E. Shells
F. Permissions (chmod, uname)
G. X-windows

A. process monitoring and control (ps -aux, ps -efl, top, kill)
B. network routing (route, netstat, ifconfig, ping, traceroute)
C. file finding (find, locate, grep, ls, tail, more, less)
D. file manipulation (rm, rmdir, mkdir)
E. file archiving (tar, gzip, zip, uncompress, bzip2)
F. using man !!!
G. Basic shell scripting (foreach)
H. Editors (vi, pico, nedit, emacs)

A. Types of issues that can be problems (local, remote, DoS)
B. Processes that don't need to be run on every computer.
C. Log files
D. Permissions (SUID/SGID)

A. Account Management
B. Filesystems
C. Daemons
D. Backups
E. RPM
F. File permissions

A. Data Types
B. File I/O (print, printf, <>, open, close)
C. Back-ticks (executing commands on the system)
D. Pattern Matching, Substitution and Replacement
E. Functions

A. Modules and Classes (how they are different)
B. Important built-in functions not previously covered (mkdir, reverse)
C. Arrays of hashes, hashes of arrays, hashes of hashes
D. BioPerl (parsing of blast reports)

A. Components
B. Devices (HD, sound, modem, NICs, video, ...)
C. CPU
D. Memory (RAM and cache)
E. Busses (PCI, ISA, IDE, SCSI - variants)
F. I/O (Serial, parallel, USB, Firewire/IEEE1394)

A. Introduction - What are they?
B. Definitions

Server, Database, Table, Field, Types, NULL, indices, identity, foreign keys, primary keys

C. SQL summary

select, insert, update, delete, joins, sub-queries, like, create table, create index, drop table

D. Brief summary of how to connect from various languages

1. Java
2. Perl
3. ISQL

A. Creating a server
B. Creating a database
C. Useful commands

1. sp_help
2. sp_helpdb
3. other sp_help*

D. Transaction log

1. "... is full". Now what?

E. Backing up the database.

A. Intro/Definitions
B. Transcription
C. Translation
D. Pedigrees (needs to be relocated)

A. cDNA libraries
B. EST sequencing
C. normalization
D. Subtraction
E. Clustering

A. What is a "disease"-gene?
B. Methods for locating/identifying disease genes.

1. Candidate
2. Positional
3. Positional-candidate

C. Information that can be useful

* Sequence, Protein domains, Functional classification, Cellular Localization, Expression, Similarity to other known genes (poss. in other organisms), Protein interactions, <just about everything>

D. Evaluating candidates

1. Looking for mutations that are correlated to the disease-state

* SSCP, Sequencing, Southern, Northern

2. Verifying candidates

* mouse-knockout, rescue in a model organism

3. Functional classification

A. Types of Mapping

1. Genetic
2. Physical

B. Genetic Mapping

C. Somatic Cell Mapping

D. Radiation Hybrid Mapping

E. Processing/Details
     A. Selection of Candidates
     B. Primer Orders
     C. Testing (and outcomes)
     D. Mapping
     E. Scoring
     F. Placement
     G. Database Loading
     H. Database Interface
     I. BLASTing
     J. comparative map construction
     K. Database Loading
     L. Database Interface

A. Summary
B. Northern Blots, Western, Immuno
C. Microarray
D. SAGE
E. Details

A. selection of probe set (summarize recent discussions)
B. rearray, sequence verification, DNA preps
C. creating the microarray slides
D. selection of target
E. target preparations
F. hybridization
G. scanning
H.image parocessing/normalize
I. data extraction
J. data analysis
K. database schema
L. database interface/tools