Revision as of 10:37, 15 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
• Evening - DEseq (Ian) http://data.marcottelab.org/XenBioinfo2014/pdf/RNAseq_recap_IQ.pdf

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)
• DESeq package home, tool for differential expression
• DESeq guide (pdf)
• Bowtie2 home, tool for read aligning
• eXpress home, tool for read quantification

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_Weka (Leon)
• ChIPseq_prep_and_map (Ian)
• Vis_with_IGV (Ian)

References

• Top 10 Algorithms in Data Mining (Knowl Inf Syst (2008) 14:1–37)

Day 6 - 5/16/2014

• Motif_analysis (Ian)
• ChIPseq_peak_calling (Ian)
• BLAST_and_sequence_analysis (Taejoon)

Day 7 - 5/17/2014

• Gene_enrichment_analysis (Virginia)
• Network_analysis (Taejoon)
• RNAseq_assembly (Taejoon)