Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Goecks, Jeremy; Nekrutenko, Anton; Taylor, James

doi:10.1186/gb-2010-11-8-r86

Cited by 3,192 publications

(2,654 citation statements)

References 28 publications

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“…Twelve mRNA libraries from one timepoint (20 h) were constructed, evaluated using a Tape Station (Agilent, Santa Clara, CA, USA), and sequenced using 50-bp single-end reads on an Illumina HiSeq2500 sequencer at the Life Sciences and Engineering Infrastructure Unit, Technion, Haifa. RNA-Seq data analysis Raw reads were uploaded onto the Galaxy platform (Goecks et al, 2010). The first 11 base pair (bp) were trimmed and the Illumina adapter sequences were clipped.…”

Section: Methodsmentioning

confidence: 99%

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

Aharonovich

Sher

2016

The ISME Journal

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Interactions between marine microorganisms may determine the dynamics of microbial communities. Here, we show that two strains of the globally abundant marine cyanobacterium Prochlorococcus, MED4 and MIT9313, which belong to two different ecotypes, differ markedly in their response to coculture with a marine heterotrophic bacterium, Alteromonas macleodii strain HOT1A3. HOT1A3 enhanced the growth of MIT9313 at low cell densities, yet inhibited it at a higher concentration, whereas it had no effect on MED4 growth. The early transcriptomic responses of Prochlorococcus cells after 20 h in co-culture showed no evidence of nutrient starvation, whereas the expression of genes involved in photosynthesis, protein synthesis and stress responses typically decreased in MED4 and increased in MIT313. Differential expression of genes involved in outer membrane modification, efflux transporters and, in MIT9313, lanthipeptides (prochlorosins) suggests that Prochlorococcus mount a specific response to the presence of the heterotroph in the cultures. Intriguingly, many of the differentially-expressed genes encoded short proteins, including two new families of co-culture responsive genes: CCRG-1, which is found across the Prochlorococcus lineage and CCRG-2, which contains a sequence motif involved in the export of prochlorosins and other bacteriocin-like peptides, and are indeed released from the cells into the media.

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Section: Methodsmentioning

confidence: 99%

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

Aharonovich

Sher

2016

The ISME Journal

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“…For comparison with H3K4me3, we used previously published data (Guenther et al, 2007) after converting that dataset to HG18 coordinates using Galaxy (Goecks et al, 2010). Statistical significance of differences in occurrence was determined using Fisher's exact test.…”

Section: Methodsmentioning

confidence: 99%

Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

Maston

Zhu

Chamberlain

et al. 2012

eLife

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The general transcription factor TFIID comprises the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex comprising TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depleting TAFs that are present or ectopically expressing TAFs that are absent, results in misregulated expression of pluripotency genes and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.DOI: http://dx.doi.org/10.7554/eLife.00068.001

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“…With the exception of the “VISUALISATION” routines (only available in the mzqViewer) – all other routines can be accessed via three different routes (i) command‐line access, which makes it possible to embed routines in other non‐Java based pipelines under any platform, e.g. Galaxy 26, (ii) Java API library for other Java applications to invoke routines directly and (iii) access from a simple graphical user interface (GUI) embedded in the mzqViewer – enabling end users to run single routines independently. We will later be releasing a full software package for proteomics analysis called ProteoSuite (http://www.proteosuite.org/), which will include the mzqLibrary, mzqViewer and quantitation by label‐free or tag‐based (iTRAQ/TMT) approaches.…”

Section: Methodsmentioning

confidence: 99%

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

Zhang

Fan

et al. 2015

Proteomics

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The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/.

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

Cited by 3,192 publications

References 28 publications

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

Transcriptional response of Prochlorococcus to co-culture with a marine Alteromonas: differences between strains and the involvement of putative infochemicals

Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard

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