User:Jhannah

From CLAB

Jay Hannah
Application Support / Development Specialist
Genetic Sequence Analysis Facility (GSAF), UNMC
Collaborative Laboratory for Applied Bioinformatics (CLAB), UNO PKI
jay@jays.net, UNMC DRC 1048, UNO PKI 253, mobile: 1-402-578-3976
Dr. Dhundy Bastola, UNO PKI 177D

• My BioPerl user page is pretty neat.

[edit] Schedule

       Mon        Tue    Wed    Thr    Fri     Sat       Sun
09                 
10                        
11     GSAF                        
12                        
13   Kiran mtg        
14                Omni   Omni   GSAF   GSAF   slack   Kiran mtg
15                       
16   PKI mtg 
17                              
18                              
19                              
20       

• UNO Bioinformatics
• Metro Articulation. Specifically: Pre-Bioinformatics.

[edit] Notes to self

• MediaWiki tips

[edit] Flash cards

As I get deeper into the science side of bioinformatics, it occurred to me that every time I just a word or phrase I don't understand I should put it on flash cards. I haven't gotten around to actually doing the cards yet, so I thought I'd start my list here.

• DNA - junk vs. trash?  :)
• EST
• RT-PCR
• histone
• oligo
• shRNA
• Rat Genome Sequence Assembly Consortium -- 3.4 is the same over 2 years
• microsatellite
• GEP - Gene Expression Profiling (just proteins)
  • CGH - Comparative Genomic Hybridization (entire genome)
    • tiling array (even more dense?)
• HMM - Hidden Markov Model
• graph theory
• chromosomes: p arms vs. q arms
• features: topological, functional, sequence-based
• motif: protein bound to DNA upsteam of a CDS that regulates the gene
  • http://en.wikipedia.org/wiki/Sequence_motif
  • http://en.wikipedia.org/wiki/Structural_motif
  • Gibbs - motif sampling program
• cytoband - the "bands" in [dia.org/wiki/Karyotype karyotyping. Also see Cytogenetics.
• UTR
• CpG island
• SINEs and LINEs
• Primer dimer prediction. I like these two tools: 1 2
• PAM-250 scoring matrix
• Scaffolds and linkage groups in the Celera Assembler aka "whole-genome shotgun (WGS) assembler software suite"
• Workflow management
  • ergatis
  • Galaxy EMBOSS tools all(?) built in
    • Condor and DAGMan
• BioBricks and Registry of Standard Biological Parts: "To express a gene, we need a promoter, RBS, and terminator."
• Synteny block: A "syntenic block" is a set of matches in which all the reference genes are located on the same reference sequence and all the query genes are located on the same query sequence.
  • Mercator (many-way genomic alignments) is what the GBrowse Synteny stuff is/was done with
  • Synteny is in chromosome space. Orthology is in genome space.
• Operon
• Artificial chromosmes: YAC (yeast), BAC (bacteria)
• Community annotation:
  • EcoliWiki
  • GMOD community annotation is a ball of MediaWiki, Chado, Apollo, VMWare.
  • Phenote  ?? OBO-Edit ??
  • Artemis can go to a Chado database. Not publicly available (yet?)
  • IGB - Integrated Genome Browser
• Clade
• SO: Sequence Ontology, OBO-Edit (Open Biomedical Ontologies)
• REST - Representational State Transfer (software architecture)
• cytochromes are involved in transduction (movement) of electrons
  • metabolism: breakdown of carbohydrates, fat, or protein
  • (cytochrome synonym for electron transfer chain)
• DNA Microarrays
  • Routine applications:
    • Gene Transcription Measurements
    • Genotyping: SNP / Mutation Detection
    • Comparitive Genomic Hybridization (cGH)
  • Niblegen has 2.1 million spots on a slide
  • ingenuity - pathway analysis software
  • heliotropism - moving towards the sun (plants)
  • oligonucleotide - 50 or so nucleotides
• ITS - Internal transcribed spacer
• automated annotation: #bioperl @ende says DIYA is "a simple annotation pipeline for microbial genomes" 'out of the box' it performs glimmer, tRNAscan-SE and rnammer (rRNAs)
• Assembly: XMFA: eXtended Multi-FastA, LCB: locally collinear block.