: [galaxy-user] Newbie: summary or metrics of Galaxy use & adoption?

This will be an interesting thread to watch

---------- Forwarded message ----------
From: "Ramon Felciano" <Feliciano ingenuity.com>
Date: May 31, 2013 2:16 AM
Subject: [galaxy-user] Newbie: summary or metrics of Galaxy use & adoption?
>
Cc:

> Hello all –
>
>  
>
> I would like to evaluate Galaxy for integration with Ingenuity's NGS analytics platform, and am trying to pull together some macro materials on how Galaxy has been used and adopted by the community at large. Are there any presentations or wiki pages that summarize basic stuff like:
>
>  
>
> # users
>
> # of deployments/ instances (public or private)
>
> Relative use of CloudMan vs locally deployed
>
> Use in any clinical or regulated environments (e.g. CLIA)
>
>  
>
> I've seen the materials at http://wiki.galaxyproject.org/Galaxy%20Project/Statistics but this looks to be only related to the public instance. Are there any similar materials that summarize across all installations, perhaps based on user surveys or the like?
>
>  
>
> Thanks in advance for your help.
>
>  
>
> Ramon
>
>  
>
> ____________________________________
>
> Ramon M. Felciano, PhD
>
> Founder and SVP, Research
>
>  
>
> INGENUITY Systems, Inc.
>
> 1700 Seaport Blvd., 3rd Floor
>
> Redwood City, CA 94063
>
> 650.381.5100 phone
>
> 650.963.3399 fax
>
>  
>
>  
>
>  
>
>
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bash script to timestamp snapshot backups of directory

modified a script from 

http://aaronparecki.com/articles/2010/07/09/1/how-to-back-up-dropbox-automatically-daily-weekly-monthly-snapshots

to be a simplified snapshot copy of the FOLDER and append the date to the folder name. Useful to have an backup on Dropbox since some files might go missing suddenly on shared folders.

#!/bin/bash
#eg.
#sh snapshot.sh FOLDER [go]
# 'go' will execute
path=Snaphotbackup-`date +%m-%b-%y`
# Run with "go" as the second CLI parameter to actually run the rsync command, otherwise prints the command that would have been run (useful for testing)
if [[ "$2" == "go" ]]
then
        rsync -avP --delete $1 $1-$path
else
        echo rsync -avP --delete $1 $1-$path
fi

Evaluation of autosomal dominant retina - PubMed Mobile

http://www.ncbi.nlm.nih.gov/m/pubmed/23687434/

METHODS: Publicly available data from the Exome Variant Project were analyzed, focusing on 36 genes known to harbor mutations causing autosomal dominant macular dystrophy.

RESULTS: Rates of rare (minor allele frequency ≤0.1%) and private missense variants within autosomal dominant retinal dystrophy genes were found to occur at a high frequency in unaffected individuals, while nonsense variants were not.

CONCLUSIONS: We conclude that rare missense variations in most of these genes identified in individuals with retinal dystrophy cannot be confidently classified as disease-causing in the absence of additional information such as linkage or functional validation.

PMID 23687434 [PubMed - as supplied by publisher]

How does your bash prompt look like?

decided to add color and full path to my bash prompt to make it easier for me to see which ssh window belongs to where absolute life saver at times when you are running several things and the tabs just don't show enough info
Plus having the user@host:/fullpath/folder in your bash prompt makes it easy to copy and paste a 'url' to scp files into that folder directly instead of typing from scratch The only downside to this is if you are buried deep in folders, you are not going to have a lot of screen estate left to type long bash commands without confusing yourself
   
My final choice:

PS1="\[\033[35m\]\t\[\033[m\]-\[\033[36m\]\u\[\033[m\]@\[\033[32m\]\h:\[\033[33;1m\]\w\[\033[m\]\$ "

image from 8 Useful and Interesting Bash Prompts - Make Tech Easier

Source:
8 Useful and Interesting Bash Prompts - Make Tech Easier
http://www.maketecheasier.com/8-useful-and-interesting-bash-prompts/2009/09/04

How to: Change / Setup bash custom prompt (PS1)
http://www.cyberciti.biz/tips/howto-linux-unix-bash-shell-setup-prompt.html

Framework for evaluating variant detection methods: comparison of aligners and callers | Blue Collar Bioinformatics

Useful info! 

Brad Chapman wrote a lengthy blog post doing a recent comparison of 3 variant callers

• FreeBayes (0.9.9 296a0fa): A haplotype-based Bayesian caller from the Marth Lab, with filtering on quality score and read depth.
• GATK UnifiedGenotyper (2.4-9): GATK's widely used Bayesian caller, using filtering recommendations for exome experiments from GATK's best practices.
• GATK HaplotypeCaller (2.4-9): GATK's more recently developed haplotype caller which provides local assembly around variant regions, using filtering recommendations for exomes from GATK's best practices.

 http://bcbio.wordpress.com/2013/05/06/framework-for-evaluating-variant-detection-methods-comparison-of-aligners-and-callers/

This evaluation work is part of a larger community effort to better characterize variant calling methods. A key component of these evaluations is a well characterized set of reference variations for the NA12878 human HapMap genome, provided by NIST's Genome in a Bottle consortium. The diagnostic component of this work supplements emerging tools like GCAT (Genome Comparison and Analytic Testing), which provides a community platform for comparing and discussing calling approaches.

I'll show a 12 way comparison between 2 different aligners (novoalign and bwa mem), 2 different post-alignment preparation methods (GATK best practices and the Marth lab's gkno pipeline), and 3 different variant callers (GATK UnifiedGenotyper, GATK HaplotypeCaller, and FreeBayes). This allows comparison of openly available methods (bwa mem, gkno preparation, and FreeBayes) with those that require licensing (novoalign, GATK's variant callers). I'll also describe bcbio-nextgen, the fully automated open-source pipeline used for variant calling and evaluation, which allows others to easily bring this methodology into their own work and extend this analysis.

PLoS One. 2013 May 8;8(5):e62355. doi: 10.1371/journal.pone.0062355. Print 2013.

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato.

Uitdewilligen JG, Wolters AM, D'hoop BB, Borm TJ, Visser RG, van Eck HJ.

Source

Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands ; The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands.

Abstract

Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1-3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60-80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.

PMID:

 

23667470

 

[PubMed - in process]

Jolie Has Double Mastectomy to Thwart Cancer Gene Risk - Bloomberg

This will have a ripple effect on genetic testing ... mastectomy ... I have no clue .. I wonder if it's possible to find the exact BRCA1 gene variant that she carries. Quite curious to see the literature on a gene variant that will make non-science people decide on invasive surgery for a '90% protection' against cancer. 

I wonder if it's really too late to do the mastectomy after you discover you have cancer .. 

Original article
http://www.bloomberg.com/news/2013-05-14/jolie-has-double-mastectomy-to-thwart-cancer-gene-risk.html

What's the gene that led to Angelina Jolie's double mastectomy? - CNN.com

http://edition.cnn.com/2013/05/14/health/jolie-what-is-brca/index.html

Opinion: Angelina Jolie's brave message - CNN.com

http://edition.cnn.com/2013/05/14/opinion/caplan-angelina-jolie-mastectomy/index.html

Opinion: Jolie's choice carries risks with benefits - CNN.com

http://edition.cnn.com/2013/05/14/opinion/carroll-jolie-mastectomy/index.html

PLOS ONE: A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062415

A multi platform approach to whole genome sequencing of novel genomes is the best way forward.  This is quite a comprehensive paper stating the steps done to achieve the final assembly with annotations.
Interestingly CLC bio was the software used  for the assembly.
It would be interesting if the assembly was 'multi platform' as well.

Article: Stranger Visions: DNA Collected from Found Objects Synthesized to Create 3D Printed Portraits

This is kinda creepy even to someone like me. 

Having your DNA sequenced (or rather typed) by a stranger to create approximate portraits of you. 

While no sinister intent is present here. It should scare the hell outta the man on the street. (Hopefully the gum spitter and butt thrower variant ) 

No doubt the project does cast human genomics in a bad light ( privacy issues) but I think a watchful public eye is good for publicly funded science. 

Stranger Visions: DNA Collected from Found Objects Synthesized to Create 3D Printed Portraits
http://www.thisiscolossal.com/2013/05/stranger-visions-dna-collected-from-found-objects-synthesized-to-create-3d-printed-portraits/

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