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iimog/biom-conversion-server
============================

Conversion tool for the biom format

1.0.6(7y ago)1716[2 issues](https://github.com/molbiodiv/biom-conversion-server/issues)MITPHP

Since Jul 8Pushed 7y ago1 watchersCompare

[ Source](https://github.com/molbiodiv/biom-conversion-server)[ Packagist](https://packagist.org/packages/iimog/biom-conversion-server)[ RSS](/packages/iimog-biom-conversion-server/feed)WikiDiscussions master Synced today

READMEChangelog (9)Dependencies (4)Versions (14)Used By (0)

biom-conversion-server
======================

[](#biom-conversion-server)

A simple php server that can convert [biom version 2 (hdf5)](http://biom-format.org/documentation/format_versions/biom-2.0.html)files and data to [biom version 1 (json)](http://biom-format.org/documentation/format_versions/biom-1.0.html)and vice versa. It simply provides a web and API interface to the convert feature of the [official python biom format tool](http://biom-format.org/index.html#installing-the-biom-format-python-package). This project is not part of the official biom project.

Please cite our article at f1000 Research that describes this module:

```
Markus J. Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, and Alexander Keller.
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format[version 2; referees: 1 approved, 2 approved with reservations].
F1000Research 2017, 5:2348. doi: 10.12688/f1000research.9618.2

```

You can cite the current version of this software repository using the Zenodo [![Zenodo](https://camo.githubusercontent.com/f33641d9e8d1a2bd28ebace9a2aae859eb8561178f83c097f83d191fb02e93f1/68747470733a2f2f7a656e6f646f2e6f72672f62616467652f31323733312f6d6f6c62696f6469762f62696f6d2d636f6e76657273696f6e2d7365727665722e737667)](https://zenodo.org/badge/latestdoi/12731/molbiodiv/biom-conversion-server)

Please cite the original biom project in addition to this project as:

```
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.
GigaScience 2012, 1:7. doi:10.1186/2047-217X-1-7

```

A public instance of the server is running at

---

- Cite Project [![DOI](https://camo.githubusercontent.com/c9a6ea42e3593414ecb0792de0a7647756c855ce9902624deb1e89d15b43028c/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f444f492d31302e3132363838253246663130303072657365617263682e393631382e322d626c75652e737667)](https://dx.doi.org/10.12688/f1000research.9618.2) and [![Zenodo](https://camo.githubusercontent.com/f33641d9e8d1a2bd28ebace9a2aae859eb8561178f83c097f83d191fb02e93f1/68747470733a2f2f7a656e6f646f2e6f72672f62616467652f31323733312f6d6f6c62696f6469762f62696f6d2d636f6e76657273696f6e2d7365727665722e737667)](https://zenodo.org/badge/latestdoi/12731/molbiodiv/biom-conversion-server)
- License [![MIT](https://camo.githubusercontent.com/08cef40a9105b6526ca22088bc514fbfdbc9aac1ddbf8d4e6c750e3a88a44dca/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f4c6963656e73652d4d49542d626c75652e737667)](https://camo.githubusercontent.com/08cef40a9105b6526ca22088bc514fbfdbc9aac1ddbf8d4e6c750e3a88a44dca/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f4c6963656e73652d4d49542d626c75652e737667)
- Build Status [![Travis](https://camo.githubusercontent.com/f8ab513ffd4d36b946663220cd4ed8b1ebb8876c029bc79bc059e8f7aeedb723/68747470733a2f2f7472617669732d63692e6f72672f6d6f6c62696f6469762f62696f6d2d636f6e76657273696f6e2d7365727665722e7376673f6272616e63683d6d6173746572)](https://travis-ci.org/molbiodiv/biom-conversion-server)
- Test Coverage [![Coveralls](https://camo.githubusercontent.com/d72a61ab050f47e5246de4b4d92d243edba4b924a31570b925f63f8221685fea/68747470733a2f2f636f766572616c6c732e696f2f7265706f732f6769746875622f6d6f6c62696f6469762f62696f6d2d636f6e76657273696f6e2d7365727665722f62616467652e7376673f6272616e63683d6d6173746572)](https://coveralls.io/github/molbiodiv/biom-conversion-server?branch=master)
- Code Climate [![CodeClimate](https://camo.githubusercontent.com/cc1054e4d74f13c38b7b8c16fa3c4e0125b087c16db61ab04006591cfd482955/68747470733a2f2f636f6465636c696d6174652e636f6d2f6769746875622f6d6f6c62696f6469762f62696f6d2d636f6e76657273696f6e2d7365727665722f6261646765732f6770612e737667)](https://codeclimate.com/github/molbiodiv/biom-conversion-server)
- Docker [![DockerPulls](https://camo.githubusercontent.com/faaf48e822619cdbc8a28b7308b40a5bcc25e1810f7784847c56a7dd01176e48/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f69696d6f672f62696f6d2d636f6e76657273696f6e2d7365727665722e7376673f6d61784167653d32353932303030)](https://hub.docker.com/r/iimog/biom-conversion-server/)

---

Getting started
---------------

[](#getting-started)

To run your own conversion server on localhost port 8080 using the docker container execute the following commands:

```
docker pull iimog/biom-conversion-server
# Use any other port by exchanging 8080 with your desired port number
docker run -d --publish 8080:80 --name biomcs iimog/biom-conversion-server

```

Now you can visit your conversion server in the browser at  And you can point tools that use the conversion api as a webservice to  (e.g. [biojs-io-biom](https://github.com/molbiodiv/biojs-io-biom)).

Changes
-------

[](#changes)

### 1.0.6 (2018-10-04)

[](#106-2018-10-04)

- Update node version in docker container
- Update required bootstrap version (CVE-2018-14041)

### 1.0.5 (2018-03-27)

[](#105-2018-03-27)

- Update biom-format to version 2.1.6

### 1.0.4 (2017-07-28)

[](#104-2017-07-28)

- Switch from bower to yarn
- Update dependencies
- Update of biojs-io-biom to version 1.0.9

### 1.0.3 (2017-03-29)

[](#103-2017-03-29)

- Update of biojs-io-biom to version 1.0.7

### 1.0.2 (2016-12-22)

[](#102-2016-12-22)

- Fix docker image

### 1.0.1 (2016-12-22)

[](#101-2016-12-22)

- Update of biojs-io-biom to version 1.0.6

### 1.0.0 (2016-09-07)

[](#100-2016-09-07)

- Update of biojs-io-biom to version 1.0.1

### 0.4.0 (2016-09-06)

[](#040-2016-09-06)

- Add details to error messages

### 0.3.0 (2016-07-29)

[](#030-2016-07-29)

- Use biojs-io-biom for UI
- Add UI to start page (file upload/download)
- Increase php server limits

### 0.2.0 (2016-07-25)

[](#020-2016-07-25)

- returned content is base64 encoded string
- require content as base64 encoded string
- handle post data passed as json
- set correct content-type header
- allow CORS requests

### 0.1.0 (2016-07-08)

[](#010-2016-07-08)

- convert to json
- convert to hdf5
- docker container
- integrate testing

###  Health Score

27

—

LowBetter than 47% of packages

Maintenance0

Infrequent updates — may be unmaintained

Popularity18

Limited adoption so far

Community7

Small or concentrated contributor base

Maturity70

Established project with proven stability

 Bus Factor1

Top contributor holds 100% of commits — single point of failure

How is this calculated?**Maintenance (25%)** — Last commit recency, latest release date, and issue-to-star ratio. Uses a 2-year decay window.

**Popularity (30%)** — Total and monthly downloads, GitHub stars, and forks. Logarithmic scaling prevents top-heavy scores.

**Community (15%)** — Contributors, dependents, forks, watchers, and maintainers. Measures real ecosystem engagement.

**Maturity (30%)** — Project age, version count, PHP version support, and release stability.

###  Release Activity

Cadence

Every ~81 days

Recently: every ~162 days

Total

11

Last Release

2826d ago

Major Versions

v0.4.0 → v1.0.02016-09-07

### Community

Maintainers

![](https://avatars.githubusercontent.com/u/7403236?v=4)[Markus J. Ankenbrand](/maintainers/iimog)[@iimog](https://github.com/iimog)

---

Top Contributors

[![iimog](https://avatars.githubusercontent.com/u/7403236?v=4)](https://github.com/iimog "iimog (160 commits)")

---

Tags

bioinformaticsbiom-format

###  Code Quality

TestsPHPUnit

Code StylePHP\_CodeSniffer

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