-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathindex.jade
213 lines (208 loc) · 8.61 KB
/
index.jade
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
.header
.header-nav
.header-nav-links
ul.header-nav-list
li
a(href="https://doc.bionode.io") Documentation
li
a(href="https://project.bionode.io") Project Board
li
a(href="https://github.com/bionode/bionode/blob/master/CONTRIBUTING.md") Contribute
li
a(href="https://github.com/bionode/bionode/issues/42") Roadmap
li
a(href="http://blog.bionode.io") Blog
a(href="https://github.com/bionode/bionode#readme", target="_blank")
.button
span.octocat
| View on GitHub
.header-logo
a(href="https://www.bionode.io") bionode
.header-info
.header-title.header-title-bigger Modular and universal bioinformatics
.header-horizontal-rule
.header-description Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatic analysis workflows.
.header-continue
a(href="#content") Find out more
span.rsaquo ›
.content#content
.content-title#About About
.content-horizontal-rule
.content-sub-container.about
p Bionode.io is an
a(href="http://blog.bionode.io") Open Source community
| building
strong highly reusable code and tools
| for bioinformatics by leveraging the Node.JS ecosystem.
p We want to process
a(href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002195") big genomic data
| using
a(href="https://github.com/substack/stream-handbook") Node.JS Streams
|.
p We welcome all kinds of
a(href="https://github.com/bionode/bionode/blob/master/CONTRIBUTING.md") contributions
| at all levels of experience, either code, knowledge, questions or suggestions.
.content#content
.content-title#Examples Examples
.content-horizontal-rule
.content-sub-container.codeExamples
code
<!--npm install bionode-ncbi -g-->
p # Download human genome
h3 $ bionode-ncbi download assembly human
<!-- npm install bionode-sra -g -->
p # Download all Sequence Read Archives for arthropoda and extract a fastq for each
h3 $ bionode-ncbi download sra arthropoda | bionode-sra fastq-dump
<!-- npm install bionode-fasta -g -->
p # Parse sequences in a fasta file into one JSON object per line, collect the ones that match chr11
h3 $ cat genome.fasta | bionode-fasta | grep chr11 | bionode-fasta --write
p # Search pubmed for ten retracted papers and use jq to view the paper's title
h3 $ bionode-ncbi search -l 10 pubmed "\"Retracted Publication\"" | jq '.title'
p # Search pubmed for papers with the word 'Cancer' in the title
h3 $ bionode-ncbi search pubmed 'Title:Cancer'
.content-subtitle.tryBioNode
h3 Try them online at
h1
a(href="http://try.bionode.io") try.bionode.io
.content-title#Features Features
.content-horizontal-rule
.content-sub-container.content-feature-cards#features
.content-feature-card
.content-card-title Scalable
.content-card-subtitle Streams are everywhere in bionode. This avoids storing intermediate data on disk or run out of memory. Building complex but reproducible pipelines is also easier with Streams
.content-feature-card
.content-card-title Universal
.content-card-subtitle Bionode runs on every platform that supports Node.js and in browsers. Along with a JavaScript API, bionode provides a CLI interface for better interactivity, and integration with other tools and languages (e.g., R, Ruby, Python)
.content-feature-card
.content-card-title Modular
.content-card-subtitle Every tool tries to do just one thing well and work independently. This gives more flexibility when building pipelines and more resolution for tracking versions and changes.
.content-title#Team
i.fa.fa-github
| Team
.content-horizontal-rule
.content-sub-container
for member in public._data.team
a(href=member.html_url)
img(src=member.avatar_url height=80 width=80)
.content-title#Community
i.fa.fa-github
| Community
.content-horizontal-rule
.content-sub-container
for member in public._data.community
a(href=member.html_url)
img(src=member.avatar_url height=80 width=80)
.content-title#Events-participants
i.fa.fa-github
| Events participants
.content-horizontal-rule
.content-sub-container
for member in public._data.events
a(href=member.html_url)
img(src="#{member.avatar_url}&s=40" height=40 width=40)
.content-title#Users Our Users
.content-horizontal-rule
.content-sub-container.content-feature-cards
.content-feature-card
img(src="images/users/afra.png")
a(href="http://afra.sbcs.qmul.ac.uk" target="_blank")
.content-card-title Afra
.content-card-subtitle Genome Annotation for the Masses - afra.sbcs.qmul.ac.uk
.content-feature-card
img(src="images/users/genevalidator.png")
a(href="http://genevalidator.sbcs.qmul.ac.uk" target="_blank")
.content-card-title GeneValidator
.content-card-subtitle Identify problems with protein-coding gene predictions.
.content-feature-card
img(src="images/users/geodiver.svg")
a(href="https://www.geodiver.co.uk" target="_blank")
.content-card-title GeoDiver
.content-card-subtitle An easy to use web tool for analysing GEO datasets.
.content-feature-card
img(src="images/users/phenopolis.png")
a(href="https://uclex.cs.ucl.ac.uk" target="_blank")
.content-card-title Phenopolis
.content-card-subtitle An Open Platform for Harmonization & Analysis of Sequencing & Phenotype Data.
.content-feature-card
img(src="images/users/repositive.png")
a(href="https://repositive.io" target="_blank")
.content-card-title Repositive.io
.content-card-subtitle One-click access to human genomic data.
.content-feature-card
img(src="images/users/openretractions.png")
a(href="http://openretractions.com" target="_blank")
.content-card-title OpenRetractions.com
.content-card-subtitle Check for retraction notices of any journal article.
.content-title#Acknowledgements Acknowledgements
.content-horizontal-rule
.content-sub-container.content-feature-cards
.content-feature-card
img(src="images/users/dat.png")
a(href="https://datproject.org" target="_blank")
.content-card-title Dat
.content-feature-card
img(src="images/users/mozillascience.svg")
a(href="https://science.mozilla.org" target="_blank")
.content-card-title Mozilla Science Lab
.content-feature-card
img(src="images/users/wurmlab.png")
a(href="https://wurmlab.github.io" target="_blank")
.content-card-title WurmLab.github.io
.content-feature-card
img(src="images/users/obf.svg")
a(href="https://www.open-bio.org" target="_blank")
.content-card-title Open Bioinformatics Foundation
.footer
.footer-directory
.footer-column
.footer-heading Explore
.footer-horizontal-rule
ul.footer-nav-list
li
span.rsaquo ›
a(href="http://www.stickermule.com/marketplace/1917-bionode-modular-and-universal-bioinformatics") Get Stickers
.footer-column
.footer-heading Learn
.footer-horizontal-rule
ul.footer-nav-list
li
span.rsaquo ›
a(href="http://try.bionode.io") Try
.footer-column
.footer-heading Connect
.footer-horizontal-rule
ul.footer-nav-list
li
a(href="https://twitter.com/bionode")
span.twitter-green
| Twitter
li
a(href="https://github.com/bionode")
span.octocat-green
| GitHub
.footer-credits
span.footer-emphasized bionode
| • 2014-2017 • design by
a(href="https://github.com/flipside-org") flipside
| for
a(href="https://datproject.org") dat
| • dat kindly granted reuse for bionode
script.
(function (i, s, o, g, r, a, m) {
i['GoogleAnalyticsObject'] = r;
i[r] = i[r] || function () {
(i[r].q = i[r].q || []).push(arguments)
}, i[r].l = 1 * new Date();
a = s.createElement(o),
m = s.getElementsByTagName(o)[0];
a.async = 1;
a.src = g;
m.parentNode.insertBefore(a, m)
})(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
ga('create', 'UA-54802258-1', 'auto');
ga('send', 'pageview');
script.
((window.gitter = {}).chat = {}).options = {
room: 'bionode/bionode'
};
script(src="//sidecar.gitter.im/dist/sidecar.v1.js", async, defer)