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October 2019

  • week 14-18:

    • organizing team: adding new organizers to the web.

  • week 7-11:

    • dev team: fixing bug in stat function, adapting sql command to mirtop
    • organizing team: adding intro to mirtop page

September 2019

  • week 16-20:

    • dev team: review integration of the SQL feature.
    • isomir meta-analysis: Finish all backup in aws S3.

  • week 9-13:

    • simulation: finish figures with all results and create table.
    • dev team: first integration of the SQL feature.
    • isomir meta-analysis: add fratta data. Backup all in S3.

August 2019

  • week 19-23:

    • simulation: analyzing S3/S4 Manatee.
    • isomir meta-analysis: adding the new samples for other studies to the results and normalizing trimming step.
    • dev team: assign projects to Arun (sql and Rshiny) and Florian (mirtop).

  • week 12-16:

    • simulation: analyzing S0/S1.
    • isomir meta-analysis: getting new samples from other experiments

  • week 01-05:

    • simulation: working on script to parse the new naming.
    • mirtop and mirgff3: working on developer team recruitment.

July 2019

  • week 21-26:
    • simulation: working on re-analysis monitoring resources
    • isomir meta-analysis: running the 3 projects that use mirxplor data and re-analyze with bowtie
  • week 14-19:
    • mirtop and mirgff3: convert to Bioinformatics format and re-submit
    • simulation: starting re-analysis monitoring resources
    • isomir meta-analysis: cleaning mirxplor references to contain sequences with H distance of 5 or more
  • week 7-12:
    • mirtop and mirgff3: final revisions and adapting the code and repository files to 1.2 version
    • simulation: continueing with S4 and S5 rounds re-analysis
  • week 1-5:
    • mirtop and mirgff3: revision of mirtop paper. Create new 1.2 version of format to add new headers. Optional genomic coordinates as output.
    • simulation: continueing with S2 and S3 rounds re-analysis
    • isomir meta-analysis: get all samples trimmed by bcbio

June 2019

  • week 24-28:
    • isomir meta-analysis: create a new repository for the analysis, get all the samples trimmed for the next step
    • simulation: move back to original cluster to normalize analysis and calculate resources
  • week 16-21:
    • isomir meta-analysis: starting getting data from last smrna kit comparison
    • simulation: creating new environment in new computer system and re-analyze new dataset
  • week 3-7:
    • simulation: discussion about repeat all in a machine, add bwa + mirtop, add S0
    • mirgff3_viz: discussion how to add deseq2 to the app
    • isomir meta-analysis: touch bases with Ioannis to see next step of synthetic

May 2019

  • week 28-31: remove nonindels from simulated bam files.
  • week 20-24: complete simulation figures. Fix mirtop issue.
  • week 13-17: adding more tools to the simulation layers. Debug mirgff3_shiny to accept big files.
  • week 5-10: automatizing simulator analysis. adding color options to mirgff3-shiny.
  • week 29Apr-2May: working on round 3 and round 4 of simulator project. First draft for Rshiny app to visualize isomiRs.

April 2019

  • week 21-26: finishing tier2 of simulator analysis.
  • week 15-19: running tier2 of simulation project.
  • week 1-5: fix issue in mirtop affecting sequences that map in the same precursor, different positions. work on more figure to show difference between synthetic and biological samples.

March 2019

  • week 25-29: preseting mirtop to BIMDC institute. Working on figure for all the data analyzed until now.
  • week 18-22: resubmitting mirtop/mirgff3 paper and debuging scripts from simulation project.
  • week 11-15: working on isomir accuracy project to present to Bioinformatics club. Fixing some issues in mirtop API suit.
  • week 4-8: work on tewari commonality for equimolar data. Starting visualization tool that uses GFF3 format.

February 2019

  • week 25-1: work on optimir compatibility and sqlite method to analyze big files.
  • week 18-22: improving mirtop to handle Manatee, exploring to work with sqlite instead of dicts.
  • week 11-15: improving mirtop to handle big bam with genomic positions. Start discussion about in person mirtop meeting.
  • week 4-8: adding new memebers. Supporting chunk files for seqbuster. Script to parse big gff3 files for simulator project.

January 2019

  • week 28-1: adapt mirtop to read in chunk BAM files from precursor hits
  • week 21-25: start the draft to put all the meta-analysis together in a google docs
  • week 14-18: communication with Illumina to figure out a plan to sequence synthetic samples
  • week 21-25: working on script to design unique synthetic sequences

December 2018

  • week 10-15: working on paper tables and merging suggestion from authors.
  • week 2-7: talk at BIG meeting in Boston. https://bluejeans.com/s/h4CR2.

November 2018

  • week 25-30: working on mirtop paper and preparing format to final review round.
  • week 12-16: design experiment for checking truncation events.
  • week 5-9: add new data set to the analysis, maybe not possible to share right now.
  • week 29-2: more modification to the mirGFF3 to addition variants. Finishing paper figure.

October 2018

  • week 22-26: Analyze Van Dijk data with spikeins to compare with current data. Update mirGFF3 definition for version 1.1.
  • week 15-19: Add mirge2.0 and custom tewari synthetic plots to equimolar analysis. Discussion about changing some ideas of the mirgff3 format.
  • week 8-12: Add gff3 to fasta. Analyze custom synthetic data from tewari set. Synthetic data analyzed by mirge2.0.
  • week 1-5: Sync the version of mirGFF3, mirtop revision paper. Comparing plasma vs equimolar: https://github.com/miRTop/incubator/blob/master/projects/tewari_equimolar/plasma_vs_equimolar.md.

September 2018

August 2018

  • week 27-31: working on figure to show the commonality among labs and replicates at the same time.
  • week 20-24: vacation time.
  • week 13-17: working on testing IDR as a possible metric for reproducibility.
  • week 6-10: first online meeting and plan for tewari re-analysis next steps. Starting the first draft for mirtop paper.

July 2018

  • week 30-2: improving log in stats command to be compatible with multiqc
  • week 16-20: discussing road map for 1/2 2018
  • week 9-13: adding compatibility with python 3

June 2018

May 2018

  • week 28-1:Fixing sRNAbench importer code.
  • week 19-25: Working on commonality figures for bcbio and miRge for tewari data.
  • week 11-16: Fixing bugs when joining miRge GFF into one file
  • week 7-8: Running tewari data with sRNAbench, PROST and isomirSEA, preparing scripts for general stats for bcbio and miRge for pilot samples.
  • week 1-4: Sharing trimmed data. Fixing --add-extra for isomiR-SEA tool

April 2018

  • week 23-27: Running data through bcbio to get trimmed data. Add extra attribute with Variants and nucleotides to allow better visual inspection.
  • week 9-13: Fixing bugs in merge and stats thanks to @AlisR.
  • week 2-6: Integrating PROST! output and updating synthetic data analysis.

March 2018

  • week 26-30: Working on benchmarking report
  • week 19-24: Adapting new sRNAbench format and discussion about PROST output
  • week 12-16: Working on abstract for BOSC2018 presented by Lorena Pantano
  • Week 5-9: Integrating PROST tools into miRTop command line

February 2018

  • Add summary function to miRTop
  • Compatibility with isomiR-SEA

January 2018

  • Analyzing synthetic data to debug tools output