Latest revision as of 13:26, 17 May 2014

Servers:

• 10.120.5.246 (main Linux server)
• 10.120.6.244 (second Linux server)
• 10.120.4.248 (Mac server)

Day 2 - 5/12/2014

• Intro_to_Unix_and_Scripting (Leon) -- http://data.marcottelab.org/XenBioinfo2014/pdf/SummerDay_LP.pdf (Lecture Note)
• Intro_to_Programming_and_Python (Taejoon)
• Awk (Leon)
• Xenopus_genome (Taejoon)

Day 3 - 5/13/2014

• Morning - RNAseq_part1 (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_intro_IQ.pdf
• Afternoon - RNAseq_part2 (Virginia) http://data.marcottelab.org/XenBioinfo2014/pdf/XenopusRNAseqLecture_VS.pdf
  • Bowtie2 home, tool for read aligning
  • eXpress home, tool for read quantification
• Evening - DEseq (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_recap_IQ.pdf
  • DESeq package home, tool for differential expression
  • DESeq guide (pdf)
  • edgeR is another program for DE analysis. It is quite similar to DESeq.

References

• Mike Gilchrist's paper for 30-min time course RNA-seq in .X tropicalis
• Mkie Blower's paper for different prep method of X. laevis egg transcripts
• Rfx2 paper (RNA-seq + ChIP-seq)

Day 4 - 5/14/2014

• Morning 1/2 - Shotgun_Proteomics_Theory (Martin)
• Morning 2/2 - Shotgun_Proteomics_Data_Process (Taejoon)
• Afternoon I - Quantitative Proteomics (Martin)
• Afternoon II - DevTimeCourse + MATLAB (Leon)
  • http://data.marcottelab.org/XenBioinfo2014/pdf/MATLAB_LP.pdf

Day 5 - 5/15/2014

• Machine_Learning_with_MATLAB (Leon)
  • http://www.cs.waikato.ac.nz/ml/weka/ (Weka is really good program. Also accompanying book is great introductory (and reference) book for machine learning, with very very minimal 'equations' (Taejoon).
• ChIPseq_prep_and_map & Visualization by IGV(Ian)
  • http://data.marcottelab.org/XenBioinfo2014/pdf/ChIP-SEQ_protocol_JCB.pdf (ChIP-seq protocol from Julie Baker lab)

References

• Top 10 Algorithms in Data Mining (Knowl Inf Syst (2008) 14:1–37)
• Chapter 8. Clustering in 'Introduction to Data Mining' by Tan, Steinbach and Kumar

Day 6 - 5/16/2014

• MATLAB (Leon)
  • http://www.mathworks.com/matlabcentral/fileexchange/32849-htk-mfcc-matlab/content/mfcc/cell2file.m
  • http://www.mathworks.com/help/matlab/import_export/write-to-delimited-data-files.html#br2ypq2-1
  • http://www.mathworks.com/matlabcentral/fileexchange/25387-write-cell-array-to-text-file
• SNP_analysis (Virginia)
• ChIPseq_motif (Ian)
• BLAST_and_sequence_analysis (Taejoon) - http://data.marcottelab.org/XenBioinfo2014/pdf/XenBioinfo2014_BLAST_TK.pdf

Day 7 - 5/17/2014

• Galaxy + GeneSet enrichment (Virginia)
  • http://genetrail.bioinf.uni-sb.de/
  • http://david.abcc.ncifcrf.gov/

• UCSC browser, etc (Ian) - http://data.marcottelab.org/XenBioinfo2014/pdf/ucsc_primer_IQ.pdf
• Microarray (Taejoon)
• Functional_Network (Taejoon)
• HowTo_MeV (Taejoon)
• Orthology (Taejoon)
• RNAseq_assembly (Taejoon)