-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathcode.html
302 lines (295 loc) · 9.95 KB
/
code.html
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
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Code | B-AMP</title>
<link rel="icon" type="image/x-icon" href="./static/images/favicon.ico">
<link rel="stylesheet" href="static/css/style.css" />
</head>
<body>
<nav>
<h1 id="siteTitle">B-AMP</h1>
<section id="navLinksSection">
<a href="index.html"><h3>Home</h3></a>
<a href="all.html"><h3>AMP Library</h3></a>
<a href="anti_gram_positive.html"><h3>Anti Gram Positive AMPs</h3></a>
<a href="anti_gram_negative.html"><h3>Anti Gram Negative AMPs</h3></a>
<a href="targets.html"><h3>Biofilm Targets</h3></a>
<a href="docked_single.html"><h3>AMPs Docked to Single Biofilm Target</h3></a>
<a href="docked_dual.html"><h3>AMPs Docked to Dual Biofilm Targets</h3></a>
<h3 id="currentPage">Code</h3>
<a href="references.html"><h3>References</h3></a>
</section>
</nav>
<div
style="
display: flex;
flex-direction: column;
justify-content: center;
align-items: center;
"
>
<h1 style="margin: 30px; font-size: 3.5em; text-align: center">Decoding our Code</h1>
<main id="codeWriteup">
<section class="codeWriteupSection">
<h1>INTRODUCTION</h1>
<p>
To prepare FASTA files from sequences, merge spreadsheets from the DRAMP
repository, sort and filter lists based on certain parameters, we used
Python code. The Python scripts utilized a
<a
target="_blank"
data-goatcounter-title="(REDIRECT) GitHub Master Spreadsheet"
1
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/utils/full.csv"
>master spreadsheet</a
>
containing relevant information; these scripts have been made open-source
and you can find them in this
<a
target="_blank"
data-goatcounter-title="(REDIRECT) GitHub KarishmaKaushikLab/B-AMP"
rel="noopener noreferrer"
href="https://github.com/KarishmaKaushikLab/B-AMP"
>GitHub repository</a
>.
</p>
</section>
<section class="codeWriteupSection">
<h1>GENERATION OF FASTA FILES</h1>
<p>
AMP sequence data was obtained from the
<a
target="_blank"
data-goatcounter-title="(REDIRECT) DRAMP"
href="http://dramp.cpu-bioinfor.org/"
>DRAMP database</a
>, an open access and manually curated database of AMP sequences. Using
these sequence strings, we generated FASTA files. For example, for Pep6 with
sequence
<pre>GNGVLKTISHECNMNTWQFLFTCC</pre>
the corresponding FASTA file would look like
<pre>>Peptide_6
GNGVLKTISHECNMNTWQFLFTCC</pre>
You can find the script for this
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/utils/fasta.py"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] FASTA"
rel="noopener noreferrer"
>here</a
>.
</p>
</section>
<section class="codeWriteupSection">
<h1>FILTERING ANTI-GRAM POSITIVE & NEGATIVE PEPTIDES</h1>
<p>
To filter AMPs peptides with anti-Gram positive and negative activities, we used scripts
which can be found
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/scripts/agp_filter/agp_filter.py"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] AG+ Filter"
rel="noopener noreferrer"
>here</a
> and <a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/scripts/agn_filter/agn_filter.py"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] AG+ Filter"
rel="noopener noreferrer"
>here</a
>, respectively. B-AMP also has a search section for anti-Gram positive and negative AMPs
<a href="/anti_gram_positive.html">here</a> and <a href="/anti_gram_negative.html">here</a>.
</p>
</section>
<section class="codeWriteupSection">
<h1>UPDATING THE AMP LISTS</h1>
<p>
To incorporate new AMP sequences into our repository, we developed a Python
script that can be found
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/scripts/dramp_combine_lists/combine.py"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] Combine Lists"
rel="noopener noreferrer"
>here</a
>.
</p>
</section>
<section class="codeWriteupSection">
<h1>SORTING RESIDUES BY INTERACTIONS</h1>
<p>
After protein-peptide docking, peptides were sorted based on interactions
and docking energy using Python's
<a
href="https://pandas.pydata.org/"
target="_blank"
data-goatcounter-title="(REDIRECT) Pandas"
rel="noopener noreferrer"
>Pandas library</a
>. You can find the code for this
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/tree/master/scripts/residue_sorter"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] Residue Sorter"
rel="noopener noreferrer"
>here</a
>.
</p>
</section>
<section class="codeWriteupSection">
<h1>GENERATING WEBSITE ASSETS & RESOURCES</h1>
<p>
This website is a static one, with no server-side code running in the cloud.
It delivers static HTML over
<a
href="https://pages.github.com/"
target="_blank"
data-goatcounter-title="(REDIRECT) GitHub Pages"
rel="noopener noreferrer"
>GitHub Pages</a
>.
</p>
<p>
To enable a search repository, we built an offline search engine in
JavaScript that runs off a compact search index. The Python script to
generate these
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/tree/master/static/js"
target="_blank"
data-goatcounter-title="(REDIRECT) [JavaScript] Search Indexes"
rel="noopener noreferrer"
>search indexes</a
>
is
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/utils/index.py"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] Index Building"
rel="noopener noreferrer"
>here</a
>.
</p>
<p>
We also wrote a
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/utils/thumbs.py"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] Thumb Generation"
rel="noopener noreferrer"
>Python script</a
>
to generate thumbnails for the 3D models on the site.
</p>
</section>
<section class="codeWriteupSection">
<h1>API SCRIPT</h1>
<p>
We also wrote a
<a
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/scripts/api_script"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] API Script"
rel="noopener noreferrer"
>script</a
>
for retrieving biofilm related literature for B-AMP peptides from the NCBI API.
</p>
</section>
<section class="codeWriteupSection">
<h1>B-AMP v2.0 API SCRIPTS</h1>
<p>
We wrote
<a
href="https://github.com/KarishmaKaushikLab/BAMP-v2-scripts"
target="_blank"
data-goatcounter-title="(REDIRECT) [Python] API Script"
rel="noopener noreferrer"
>scripts</a> to retrieve available data of the biofilm targets from the UniProt, PDB and PubMed databases.
</p>
</section>
</main>
</div>
<footer>
<img src="static/images/kaushik-lab-logo.png" id="labLogo" />
<section id="footerContent">
<p>A project by</p>
<h1>HUMAN-RELEVANT INFECTION BIOLOGY GROUP</h1>
<h2>(led by Dr. Karishma Kaushik)</h2>
<hr />
<section class="footerLinks">
<a
href="https://www.karishmakaushiklab.com/"
target="_blank"
data-goatcounter-title="(REDIRECT) karishmakaushiklab.com"
rel="noopener noreferrer"
>
<img src="static/icons/globe.png" class="footerLink" />
</a>
<a
href="https://twitter.com/KaushikLab"
target="_blank"
data-goatcounter-title="(REDIRECT) Twitter @KaushikLab"
rel="noopener noreferrer"
>
<img src="static/icons/twitter.png" class="footerLink" />
</a>
<a
href="mailto:karishmaskaushik@gmail.com"
target="_blank"
data-goatcounter-title="(EMAIL) karishmaskaushik@gmail.com"
rel="noopener noreferrer"
>
<img src="static/icons/mail.png" class="footerLink" />
</a>
<a
href="https://github.com/KarishmaKaushikLab/B-AMP"
target="_blank"
data-goatcounter-title="(REDIRECT) GitHub KarishmaKaushikLab/B-AMP"
rel="noopener noreferrer"
>
<img src="static/icons/github.png" class="footerLink" />
</a>
</section>
</section>
</footer>
<section id="license">
<p>
This work is licensed under a
<a
rel="license"
style="color: white"
href="https://creativecommons.org/licenses/by/3.0/deed.en_US"
rel="noopener noreferrer"
target="_blank"
data-goatcounter-title="(REDIRECT) CC3 License"
>Creative Commons Attribution 3.0 Unported License</a
>, with the exception of this website's code and additional utility code that aided
this work, which is separately licensed under the
<a
rel="license"
style="color: white"
href="https://github.com/KarishmaKaushikLab/B-AMP/blob/master/LICENSE"
rel="noopener noreferrer"
target="_blank"
data-goatcounter-title="(REDIRECT) GitHub License GPLv3"
>GNU General Public License v3.0</a
>.
</p>
</section>
<script
data-goatcounter="https://b-amp.goatcounter.com/count"
async
src="//gc.zgo.at/count.js"
></script>
<script>
// Track outgoing clicks using GoatCounter
const outgoingLinks = document.querySelectorAll('a[target="_blank"]');
for (const outgoingLink of outgoingLinks) {
outgoingLink.setAttribute("data-goatcounter-click", outgoingLink.href);
}
</script>
</body>
</html>