Lab notebook

Welcome to my open science lab notebook. For an introduction, acknowledgements and technical details, see my first post. Updates to my workflow after 3 months of use are here.

Caveat emptor. Please keep in mind that these are rough lab notes recorded for reproducibility and my own reference. They likely contain mistakes, which are solely mine. If, perchance, you find this information useful or interesting, drop me a line!

16 October 2014 Leaving the academic canyon
30 September 2014 DNA extraction for PacBio
29 September 2014 DNA extraction for PacBio
19 September 2014 Friday notes
18 September 2014 Thursday notes
17 September 2014 Wednesday notes
16 September 2014 Tuesday notes
15 September 2014 Monday notes
12 September 2014 Running RStudio in the cloud
11 September 2014 RADseq fastqc
10 September 2014 Wednesday 10 September notes
09 September 2014 Tuesday 9 September notes
08 September 2014 Monday 8 September notes
05 September 2014 2 - 5 September notes
29 August 2014 25 -- 29 August notes
22 August 2014 18 -- 22 August notes
15 August 2014 11 -- 15 August notes
08 August 2014 4 -- 8 August notes
07 August 2014 August Aphaenophone conference call
01 August 2014 Friday August 1 week's notes
28 July 2014 Monday July 28 notes
25 July 2014 July 21- July 25 notes
18 July 2014 July 14 - July 18 notes
27 June 2014 ddRADseq success
24 June 2014 Evolution 2014 notes
20 June 2014 Monday July 28 notes
13 June 2014 Monday June 9 - Friday June 13 notes
06 June 2014 Friday June 6 notes
05 June 2014 GO semantic similarity
04 June 2014 RDAVIDWebService debugging
03 June 2014 Tuesday June 3 notes
02 June 2014 Installing Jekyll 2.0
30 May 2014 May 26 - 30 notes
23 May 2014 May 20 - 23 notes
21 May 2014 rDAVIDWebService Installation
19 May 2014 Ubuntu 12.04 System Configuration
16 May 2014 May 12 - 16 notes
09 May 2014 May 5 - 9 notes
02 May 2014 Friday ddRADseq debugging
01 May 2014 Thursday notes
29 April 2014 ddRADseq debugging
28 April 2014 Monday notes
25 April 2014 Friday notes
24 April 2014 Thursday notes
23 April 2014 ddRADseq round 2 summary
22 April 2014 Tuesday notes
21 April 2014 Monday notes
18 April 2014 Friday notes
17 April 2014 Thursday April 17 notes
16 April 2014 Wednesday April 16 notes
15 April 2014 ddRADseq trial 2
14 April 2014 Monday notes
11 April 2014 Notes
04 April 2014 Notes
28 March 2014 Notes
27 March 2014 Notes
27 March 2014 Making a bibliography with Pandoc
26 March 2014 Using ESS with .Rmd files
25 March 2014 Tuesday notes
24 March 2014 ddRADseq PCR amplification
21 March 2014 ddRADseq Dynabeads
20 March 2014 ddRADseq Dynabeads
19 March 2014 Summary of statistical survey results
19 March 2014 A rant on the academic job search
19 March 2014 ddRADseq size selection
18 March 2014 Monday notes
12 March 2014 ddRADseq ligation
10 March 2014 Monday notes
07 March 2014 Friday notes
06 March 2014 ddRADseq anneal adapters
05 March 2014 Intermediate-expression - biological interpretation
04 March 2014 March 3 - 4 notes
28 February 2014 February 28 notes
23 February 2014 Aphaenofest III
21 February 2014 February 17 - 21 notes
14 February 2014 February 10 - 14 notes
07 February 2014 February 3 - 7 notes
30 January 2014 Thursday notes
29 January 2014 Wednesday notes
28 January 2014 Tuesday notes
27 January 2014 Monday notes
24 January 2014 Thursday - Friday notes
22 January 2014 Wednesday notes
21 January 2014 Tuesday notes
20 January 2014 Monday notes
17 January 2014 Wednesday notes
15 January 2014 Wednesday notes
14 January 2014 Tuesday notes
13 January 2014 Monday notes
10 January 2014 Thursday - Friday notes
08 January 2014 Wednesday Jan 8
07 January 2014 Tuesday Jan 7
06 January 2014 Monday Jan 6 notes
03 January 2014 Friday Jan 3
02 January 2014 Thursday Jan 2
31 December 2013 BLAST notes
31 December 2013 2013 Annual Report
23 December 2013 Monday notes
12 December 2013 Tuesday - Thursday notes
09 December 2013 Tuesday - Thursday notes
06 December 2013 Wed - Fri notes
04 December 2013 ddRADseq enzyme selection
03 December 2013 Tuesday notes
02 December 2013 Monday notes
25 November 2013 Mon notes
22 November 2013 Wed - Fri notes
19 November 2013 Why I use Zotero
18 November 2013 Teaching
15 November 2013 Wed - Fri notes
13 November 2013 Thoughts on methods to detect selection along environmental gradients
12 November 2013 Wednesday notes
11 November 2013 Monday notes
08 November 2013 Qiagen Genomic-tip extraction for ants
08 November 2013 Friday notes
07 November 2013 Thursday notes
06 November 2013 Wednesday notes
05 November 2013 Meeting with VGN notes
04 November 2013 Monday notes
01 November 2013 Week's notes
24 October 2013 Summary of Aphaenogaster transcriptome assembly and gene expression analysis
23 October 2013 Monday - Wednesday notes
18 October 2013 Thursday - Friday notes
16 October 2013 Wednesday notes
15 October 2013 Tuesday notes
14 October 2013 Monday notes
11 October 2013 Mapping reads to de novo assembly
10 October 2013 de novo gene expression mapping works!
09 October 2013 More transcriptome simulation notes
08 October 2013 Transcriptome simulation notes
07 October 2013 Tuesday 8 October
04 October 2013 Week Notes 30 September - 4 October
27 September 2013 Week Notes 23-27 September
26 September 2013 Transcriptome assembly with digital normalization and read merging
20 September 2013 Week Notes 16-20 September
13 September 2013 Week Notes 9-13 September
06 September 2013 Week Notes 2-6 September
04 September 2013 A wager with Rob Dunn
04 September 2013 ApGXL Heat Shock Protocol
23 August 2013 Friday 23 August
22 August 2013 Thursday 22 August
21 August 2013 Wednesday 21 August
20 August 2013 Tuesday notes
16 August 2013 Week's notes August 16
12 August 2013 Resources to learn R
30 July 2013 Transcriptome assembly notes
26 July 2013 RNAseq read filtering prior to assembly
25 July 2013 Running velvet
24 July 2013 RNAseq QC
19 July 2013 Gordon Conference
12 July 2013 Update on open lab notebook
12 July 2013 Projects
11 July 2013 Summary of sample treatment for transcriptomic studies
10 July 2013 Reviews
03 July 2013 Notes for week of July 1
28 June 2013 Notes for week of June 24
21 June 2013 Notes for week of June 17
14 June 2013 Notes for week of June 10
09 June 2013 Aphaenofest Day 1
06 June 2013 week notes
30 May 2013 week notes
24 May 2013 Statistical methods survey
21 May 2013 Tuesday notes
20 May 2013 Monday bioinformatics
16 May 2013 Thursday notes
15 May 2013 Field work
14 May 2013 Tuesday notes
13 May 2013 Monday May 13 notes
10 May 2013 week notes
08 May 2013 Finding Aphaenogaster
07 May 2013 Antlab workstation guidelines
07 May 2013 Monday notes
23 April 2013 Aphaenogaster QC report for Illumina
22 April 2013 Monday
19 April 2013 Friday
18 April 2013 SAM pileup!
17 April 2013 Wednesday
16 April 2013 Resubmitting
15 April 2013 Thinking about P-values
12 April 2013 Bowtie2
11 April 2013 Thursday
10 April 2013 still assembling
09 April 2013 Velvet needs shuffled files!
08 April 2013 Bioinformatics Monday
05 April 2013 Friday
04 April 2013 fastq
03 April 2013 Reflections on “Insights from population genetics for range limits of a widely-distributed annual plant”
03 April 2013 Completing permit commitments
02 April 2013 Starting BioPython
01 April 2013 April Fool's notes
29 March 2013 permits and genome assembly
28 March 2013 RNAseq simulation
27 March 2013 wednesday
21 March 2013 RNA extraction
13 March 2013 starting an open lab notebook