Blackbird is currently on hold

The changes to Phinch introduced by Blackbird are going to be merged into the main Phinch project (see #63 and #67). Blackbird will retire after those changes are merged. Future development will happen in the Phinch repository and it's fork At https://blackbird.iimog.org there is a preview of Phinch after merging the pull request.

Server

A public server is online at https://blackbird.iimog.org. But you can also host your own (see below).

About Blackbird

This fork is based on Phinch 1.1.2. It addresses a couple of practical limitations. All changes are made available under the same license as the original project (BSD 2-clause). Here is an overview of the changes between Blackbird 1.2.0 and Phinch 1.1.2:

• All desktop browsers are allowed (original project only allows Chrome)
• BIOM format version 2 is supported (in addition to version 1) by integrating biom-conversion-server and biojs-io-biom
• Export is possible as svg and png format (Phinch#43)
• Dense biom format is supported (in addition to sparse, Phinch#64)
• A few bugs are fixed (e.g. Phinch#49)
• Shared links are not sent via email automatically
• A docker image is provided for self hosting
• SQLite instead of MySQL is used

I'll be happy to help port my changes back to the main project.

About the original project

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Davis. Whether it's genes, proteins, or microbial species, Phinch provides an interactive visualization tool that allows users to explore and manipulate large biological datasets.

Phinch is optimized for use in the Chrome browser. It currently supports downstream analyses of .biom files (Biological Observation Matrix, a JSON-formatted file type typically used to represent marker gene OTUs or metagenomic data). All sample metadata and taxonomy/ontology information MUST be embedded in the .biom file before being uploaded.

Cite

If you use Blackbird for your research please cite this repository (by doi, see below) as well as the following articles:

Ankenbrand MJ, Terhoeven N, Hohlfeld S et al. biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format [version 1; referees: awaiting peer review] F1000Research 2016, 5:2348; doi:10.12688/f1000research.9618.1

and

Phinch: An interactive, exploratory data visualization framework for –Omic datasets. Holly M Bik, Pitch Interactive. bioRxiv 009944; doi:10.1101/009944

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• Cite Project
• License
• Docker

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Data

Blackbird supports both "sparse" and "dense" BIOM formats (although sparse .biom files are highly recommended, since the file size is much smaller). In QIIME, users can prepare the .biom file by executing the following commands:

make_otu_table.py -i final_otu_map_mc2.txt -o otu_table_mc2_w_tax.biom -t rep_set_tax_assignments.txt

Second, add your sample metadata to your .biom file. Where your input file (-i) is your OTU Map (defining clusters of raw sequences reads), taxonomy file (-t) contains the taxonomy or gene ontology strings that correspond to each OTU, and mapping file (-m) is a tab-delimited file containing sample metadata (instructions).

biom add-metadata -i otu_table_mc2_w_tax.biom -o otu_table_mc2_w_tax_and_metadata.biom -m sample_metadata_mapping_file.txt

Run your own Blackbird server

Use docker to run your own Blackbird server locally:

# run on port 8081 (for another free port exchange the 8081 with that port number)
docker run -d --publish 8081:80 --name blackbird iimog/blackbird

You can then navigate your web browser to http://localhost:8081/.

Libraries

D3: http://d3js.org/
IndexedDB: http://aaronpowell.github.io/db.js/
FileSaver: https://github.com/eligrey/FileSaver.js/
Moment: http://momentjs.com/
jQuery: http://jquery.com/
jQueryUI: http://jqueryui.com/
jQueryFracs: http://larsjung.de/fracs/
Blob: https://github.com/eligrey/Blob.js/
DataTable: https://datatables.net/
JSZip: http://stuk.github.io/jszip/
Lo-Dash: http://lodash.com/
lz-string: https://github.com/pieroxy/lz-string
md5-js: https://github.com/wbond/md5-js
biom-conversion-server: https://github.com/molbiodiv/biom-conversion-server
biojs-io-biom: https://github.com/molbiodiv/biojs-io-biom

License

The BSD 2-Clause License

Logo

The Blackbird logo slightly resembles the Phinch logo using the Blackbird-Silhouette from openclipart.org (public domain) and the Hanken font from fontlibrary.org (SIL Open Font License).

Changes

v1.2.2 (2016-10-17)

• Add footer to all pages
• Fix sharing permissions
• Fix svg namespace

v1.2.1 (2016-09-08)

• Fix security problem
• Add info and opt-out for Google Analytics

v1.2.0 (2016-09-07)

• First release as Blackbird (previously Phinch)
• All desktop browsers are allowed (original project only allows Chrome)
• BIOM format version 2 is supported (in addition to version 1) by integrating biom-conversion-server and biojs-io-biom
• Export is possible as svg and png format (Phinch#43)
• Dense biom format is supported (in addition to sparse, Phinch#64)
• A few bugs are fixed (e.g. Phinch#49)
• Shared links are not sent via email automatically
• A docker image is provided for self hosting
• SQLite instead of MySQL is used