Journal: Journal of Synchrotron Radiation

Article Title: Mamba : a systematic software solution for beamline experiments at HEPS

doi: 10.1107/S1600577522002697

Figure Lengend Snippet: An example IPython startup script for Mamba .

Article Snippet: Since Bluesky recommends the IPython (Pérez & Granger, 2007 ) interactive command line interface (CLI) of Python for its regular use on beamlines, we designed Mamba with cooperation between the CLI ( Mamba backend) and our GUIs ( Mamba frontend) in mind; inspired by AutoCAD -like software (called ‘parametric modeling software’ in its industry), we extensively use what we call ‘command injection’ (Fig. 1 ) to implement this cooperation.

Techniques:

Journal: Histochemistry and Cell Biology

Article Title: Online citizen science with the Zooniverse for analysis of biological volumetric data

doi: 10.1007/s00418-023-02204-6

Figure Lengend Snippet: Further resources relevant to developing a Zooniverse citizen science project

Article Snippet: Panoptes command-line interface , github.com/zooniverse/panoptes-cli/blob/master/README.md.

Techniques: Virus

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Biological knowledge building process enabled by Confero which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques:

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Confero platform overview. Depicts where Confero fits into a typical high-throughput transcriptomics analysis workflow. Contrast data is fed into the platform after the statistical analysis step where it is then converted to idMAPS format and loaded using Confero tools. Contrast data is automatically processed and stored and gene sets are extracted. Data can be analyzed for gene set enrichment and results can be used in other Confero tools or exported for other analyses.

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques: High Throughput Screening Assay

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file : Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques: Functional Assay

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Screenshot of the Estrogen gene set entry in the Confero DB. Clicking on a gene set hyperlink (e.g. BMC_Bioconductor_Estrogen_PW_[Estro10]_UP) enables to access detailed information such as the rank of the genes extracted from the contrast, the Entrez gene ID, the gene symbol and description.

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques:

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Screenshot of the report following importing and processing of the Bioconductor estrogen contrast data in Confero using Galaxy. The report shows 1) whether contrast data have been correctly imported and processed (several checks during the mapping and collapsing process reported at the top of the document (“Check/Map/Collapse Contrast Dataset Report”), 2) information on the gene sets that have been automatically extracted from each contrast and stored (UP, DN, and AR gene sets) in the Confero DB (“Gene Set Report”). As example (see also Figure ), 169, 105 and 274 most significantly up- , down- and all-regulated genes (FDR<0.05) were respectively extracted as gene sets UP, DN and AR from the contrast data “Estro10” (comparison of gene expression levels of estrogen vs control samples collected at 10h).

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques: Comparison, Gene Expression, Control

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Screenshot of the Estrogen contrast dataset entry in the Confero DB. To access a database Estrogen Contrast data entry, the “View and Manage Data” tool is selected in the toolbox (left frame) and the appropriate contrast dataset name can be chosen in the available list. The entry contains information on the contrast dataset at the top (e.g. “BMC_Bioconductor_Estrogen_PW”), contrasts (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]”) and associated gene sets at the bottom (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]_UP”). Details and data files can be accessed via the hyperlinks. Data files can be saved locally upon needs.

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques:

Journal: BMC Genomics

Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

doi: 10.1186/1471-2164-14-514

Figure Lengend Snippet: Summary of Confero Bioconductor estrogen dataset GSEA results and leveraging of leading edge genes results from Export Leading Edge Matrix tool. Grouping gene sets per biological processes and investigating the leading edge genes associated to significantly enriched gene sets enables to rapidly interpret biological events at the molecular level and raise new hypothesis that could further be experimentally verified. Red and green colors highlight normalized enrichment scores that are significantly enriched for up- or down-regulated genes, respectively.

Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

Techniques: