bíogo

bíogo: a simple high-performance bioinformatics toolkit for the Go language - Published in JOSS (2017)

https://github.com/biogo/biogo

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 6 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: biorxiv.org, nature.com
✓
Committers with academic emails
3 of 17 committers (17.6%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Scientific Fields

Engineering Computer Science - 40% confidence

Last synced: 4 months ago · JSON representation

Repository

biogo is a bioinformatics library for Go

Basic Info

Host: GitHub
Owner: biogo
License: bsd-3-clause
Language: Go
Default Branch: master
Homepage:
Size: 3.96 MB

Statistics

Stars: 400
Watchers: 30
Forks: 51
Open Issues: 7
Releases: 0

Created almost 11 years ago · Last pushed over 1 year ago

Metadata Files

Readme Contributing Funding License Authors Codemeta

Installation

    $ go get github.com/biogo/biogo/...

Overview

bíogo is a bioinformatics library for the Go language.

Getting help

Help or similar requests are preferred on the biogo-user Google Group.

https://groups.google.com/forum/#!forum/biogo-user

Contributing

If you find any bugs, feel free to file an issue on the github issue tracker. Pull requests are welcome, though if they involve changes to API or addition of features, please first open a discussion at the biogo-dev Google Group.

https://groups.google.com/forum/#!forum/biogo-dev

Citing

If you use bíogo, please cite Kortschak, Snyder, Maragkakis and Adelson "bíogo: a simple high-performance bioinformatics toolkit for the Go language", doi:10.21105/joss.00167, and Kortschak and Adelson "bíogo: a simple high-performance bioinformatics toolkit for the Go language", doi:10.1101/005033.

The Purpose of bíogo

bíogo stems from the need to address the size and structure of modern genomic and metagenomic data sets. These properties enforce requirements on the libraries and languages used for analysis:

speed - size of data sets
concurrency - problems often embarrassingly parallelisable

In addition to the computational burden of massive data set sizes in modern genomics there is an increasing need for complex pipelines to resolve questions in tightening problem space and also a developing need to be able to develop new algorithms to allow novel approaches to interesting questions. These issues suggest the need for a simplicity in syntax to facilitate:

ease of coding
checking for correctness in development and particularly in peer review

Related to the second issue is the reluctance of some researchers to release code because of quality concerns.

The issue of code release is the first of the principles formalised in the Science Code Manifesto.

Code  All source code written specifically to process data for a published
      paper must be available to the reviewers and readers of the paper.

A language with a simple, yet expressive, syntax should facilitate development of higher quality code and thus help reduce this barrier to research code release.

Articles

bíogo: a simple high-performance bioinformatics toolkit for the Go language

Analysis of Illumina sequencing data using bíogo

Using and extending types in bíogo

Yet Another Bioinformatics Library

It seems that nearly every language has it own bioinformatics library, some of which are very mature, for example BioPerl and BioPython. Why add another one?

The different libraries excel in different fields, acting as scripting glue for applications in a pipeline (much of [1, 2, 3]) and interacting with external hosts [1, 2, 4, 5], wrapping lower level high performance languages with more user friendly syntax [1, 2, 3, 4] or providing bioinformatics functions for high performance languages [5, 6].

The intended niche for bíogo lies somewhere between the scripting libraries and high performance language libraries in being easy to use for both small and large projects while having reasonable performance with computationally intensive tasks.

The intent is to reduce the level of investment required to develop new research software for computationally intensive tasks.

BioPerl http://genome.cshlp.org/content/12/10/1611.full http://www.springerlink.com/content/pp72033m171568p2
BioPython http://bioinformatics.oxfordjournals.org/content/25/11/1422
BioRuby http://bioinformatics.oxfordjournals.org/content/26/20/2617
PyCogent http://genomebiology.com/2007/8/8/R171
BioJava http://bioinformatics.oxfordjournals.org/content/24/18/2096
SeqAn http://www.biomedcentral.com/1471-2105/9/11

Library Structure and Coding Style

The bíogo library structure is influenced both by the Go core library.

The coding style should be aligned with normal Go idioms as represented in the Go core libraries.

Quality Scores

Quality scores are supported for all sequence types, including protein. Phred and Solexa scoring systems are able to be read from files, however internal representation of quality scores is with Phred, so there will be precision loss in conversion. A Solexa quality score type is provided for use where this will be a problem.

Copyright and License

BITSTREAM CHARTER is a registered trademark of Bitstream Inc.

Owner

Name: bíogo
Login: biogo
Kind: organization

Repositories: 14
Profile: https://github.com/biogo

bíogo is a bioinformatics library collection for Go

JOSS Publication

bíogo: a simple high-performance bioinformatics toolkit for the Go language

Published

February 18, 2017

DOI

10.21105/joss.00167

Volume 2, Issue 10, Page 167

Authors

R Daniel Kortschak

School of Biological Sciences, The University of Adelaide

Josh Bleecher Snyder

None

Manolis Maragkakis

Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania

David L. Adelson

School of Biological Sciences, The University of Adelaide

Editor

Pjotr Prins

CodeMeta (codemeta.json)

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      "name": "R Daniel Kortschak",
      "affiliation": "School of Biological Sciences, The University of Adelaide"
    },
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      "name": "Josh Bleecher Snyder",
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      "@type": "Person",
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      "name": "Manolis Maragkakis",
      "affiliation": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania"
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      "@id": "http://orcid.org/0000-0003-2404-5636",
      "@type": "Person",
      "email": "david.adelson@adelaide.edu.au",
      "name": "David L Adelson",
      "affiliation": "School of Biological Sciences, The University of Adelaide"
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  "codeRepository": "https://github.com/biogo/biogo",
  "datePublished": "2017-01-05",
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  "dateCreated": "2017-01-05",
  "description": "a simple high-performance bioinformatics toolkit for the Go language",
  "keywords": "bioinformatics, toolkit, golang",
  "license": "BSD-3 like",
  "title": "bíogo",
  "version": "v1.0.1"
}

GitHub Events

Total

Watch event: 16
Fork event: 2

Last Year

Watch event: 16
Fork event: 2

Committers

Last synced: 5 months ago

All Time

Total Commits: 503
Total Committers: 17
Avg Commits per committer: 29.588
Development Distribution Score (DDS): 0.258

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
kortschak	d**k@a**u	373
kortschak	k**k@z**u	92
Josh Bleecher Snyder	j**n@g**m	14
Emmanouil "Manolis" Maragkakis	m**g@g**m	5
Gordon Gremme	g**n@g**g	4
Jason	j**s@t**g	2
Davor Kapsa	d**a@g**m	2
Olga Botvinnik	o**k@g**m	2
Harry Scells	h**s@g**m	1
Clayton Wheeler	c**r@g**m	1
Brent Pedersen (brentp)	b**e@g**m	1
Brennon Loveless	b**t@b**m	1
Jason Travis	J**s@n**u	1
Peter Mattis	p**s@g**m	1
Santiago Castro	s**0@h**m	1
Yasushi Saito	y**o@g**m	1
aboffin	p**k@g**m	1

Committer Domains (Top 20 + Academic)

nau.edu: 1 bayer.com: 1 genomenon.com: 1 tgen.org: 1 gremme.org: 1 zoidberg.mbs.adelaide.edu.au: 1 adelaide.edu.au: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 47
Total pull requests: 43
Average time to close issues: about 1 month
Average time to close pull requests: 2 days
Total issue authors: 20
Total pull request authors: 16
Average comments per issue: 3.06
Average comments per pull request: 2.26
Merged pull requests: 41
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

GoogleCodeExporter (21)
brentp (3)
kortschak (3)
josharian (2)
nileshpatra (2)
bsipos (2)
mys721tx (1)
DanielRivasMD (1)
thomas-bio (1)
YspCoder (1)
ygidtu (1)
srynobio (1)
mnsmar (1)
mariokostelac (1)
sis6789 (1)

Pull Request Authors

kortschak (18)
corburn (4)
mnsmar (4)
olgabot (2)
dvrkps (2)
josharian (2)
bloveless (2)
gordon (2)
hscells (1)
aboffin (1)
bryant1410 (1)
yxzzy-wtf (1)
petermattis (1)
yasushi-saito (1)
brentp (1)

Top Labels

Issue Labels

auto-migrated (21) Priority-Medium (20) Type-Defect (18) Type-Enhancement (3) unfortunate (1) Priority-Low (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads: unknown
Total docker downloads: 116,924

Total dependent packages: 19
Total dependent repositories: 20
Total versions: 5

proxy.golang.org: github.com/biogo/biogo

bíogo is a bioinformatics library for the Go language. It is a work in progress. bíogo stems from the need to address the size and structure of modern genomic and metagenomic data sets. These properties enforce requirements on the libraries and languages used for analysis: In addition to the computational burden of massive data set sizes in modern genomics there is an increasing need for complex pipelines to resolve questions in tightening problem space and also a developing need to be able to develop new algorithms to allow novel approaches to interesting questions. These issues suggest the need for a simplicity in syntax to facilitate: Related to the second issue is the reluctance of some researchers to release code because of quality concerns http://www.nature.com/news/2010/101013/full/467753a.html The issue of code release is the first of the principles formalised in the Science Code Manifesto http://sciencecodemanifesto.org/ A language with a simple, yet expressive, syntax should facilitate development of higher quality code and thus help reduce this barrier to research code release. It seems that nearly every language has it own bioinformatics library, some of which are very mature, for example BioPerl and BioPython. Why add another one? The different libraries excel in different fields, acting as scripting glue for applications in a pipeline (much of [1-3]) and interacting with external hosts [1, 2, 4, 5], wrapping lower level high performance languages with more user friendly syntax [1-4] or providing bioinformatics functions for high performance languages [5, 6]. The intended niche for bíogo lies somewhere between the scripting libraries and high performance language libraries in being easy to use for both small and large projects while having reasonable performance with computationally intensive tasks. The intent is to reduce the level of investment required to develop new research software for computationally intensive tasks. The bíogo library structure is influenced both by the structure of BioPerl and the Go core libraries. The coding style should be aligned with normal Go idioms as represented in the Go core libraries. Position numbering in the bíogo library conforms to the zero-based indexing of Go and range indexing conforms to Go's half-open zero-based slice indexing. This is at odds with the 'normal' inclusive indexing used by molecular biologists. This choice was made to avoid inconsistent indexing spaces being used — one-based inclusive for bíogo functions and methods and zero-based for native Go slices and arrays — and so avoid errors that this would otherwise facilitate. Note that the GFF package does allow, and defaults to, one-based inclusive indexing in its input and output of GFF files. Quality scores are supported for all sequence types, including protein. Phred and Solexa scoring systems are able to be read from files, however internal representation of quality scores is with Phred, so there will be precision loss in conversion. A Solexa quality score type is provided for use where this will be a problem. Copyright ©2011-2012 The bíogo Authors except where otherwise noted. All rights reserved. Use of this source code is governed by a BSD-style license that can be found in the LICENSE file.

Homepage: https://github.com/biogo/biogo
Documentation: https://pkg.go.dev/github.com/biogo/biogo#section-documentation
License: BSD-3-Clause
Latest release: v1.0.4
published about 4 years ago

Versions: 5
Dependent Packages: 19
Dependent Repositories: 20
Docker Downloads: 116,924

Rankings

Docker downloads count: 0.8%

Dependent packages count: 1.1%

Dependent repos count: 1.2%

Average: 2.0%

Stargazers count: 3.0%

Forks count: 3.6%

Last synced: 4 months ago

Dependencies

go.mod go

github.com/biogo/graph v0.0.0-20150317020928-057c1989faed
github.com/biogo/hts v1.1.0
github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83
gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15

go.sum go

dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9
github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802
github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1
github.com/biogo/graph v0.0.0-20150317020928-057c1989faed
github.com/biogo/hts v1.1.0
github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83
github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72
github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560
github.com/kr/pretty v0.2.0
github.com/kr/pty v1.1.1
github.com/kr/text v0.1.0
github.com/ulikunitz/xz v0.5.6
golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2
golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529
golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8
golang.org/x/exp v0.0.0-20200119233911-0405dc783f0a
golang.org/x/image v0.0.0-20190227222117-0694c2d4d067
golang.org/x/image v0.0.0-20190802002840-cff245a6509b
golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028
golang.org/x/mod v0.1.0
golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3
golang.org/x/net v0.0.0-20190620200207-3b0461eec859
golang.org/x/sync v0.0.0-20190423024810-112230192c58
golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a
golang.org/x/sys v0.0.0-20190312061237-fead79001313
golang.org/x/sys v0.0.0-20190412213103-97732733099d
golang.org/x/text v0.3.0
golang.org/x/tools v0.0.0-20191012152004-8de300cfc20a
golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7
gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15

bíogo

Science Score: 95.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

bíogo

Installation

Overview

Getting help

Contributing

Citing

The Purpose of bíogo

Articles

Yet Another Bioinformatics Library

Library Structure and Coding Style

Quality Scores

Copyright and License

Owner

JOSS Publication

bíogo: a simple high-performance bioinformatics toolkit for the Go language

Authors

Editor

Tags

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/biogo/biogo

Rankings

Dependencies