OpenLAB / RepTB

Download as
Browse Code ยป

Commit 624f93a94a98a753bf310093e428facced178ac3

Authored by anurag
1 parent d12d87ddbb
Exists in master

Updated License and README

Showing 4 changed files with 68 additions and 87 deletions   Show diff stats
LICENSE.html
View file @d12d87d
... ... @@ -1,38 +0,0 @@
1   -<!DOCTYPE html>
2   -<html>
3   -<body>
4   -
5   -
6   -<h1>RepTB License</h1>
7   -<div class="two columns alpha">
8   -<img src="https://licensebuttons.net/l/by/3.0/88x31.png" alt="" width="88" height="31">
9   -</div>
10   -
11   -
12   -Copyright (c) 2018 Anshu Bhardwaj
13   -
14   -
15   -<p>Permission is hereby granted, free of charge, to any person obtaining a copy
16   -of RepTB (the Software) and associated documentation files, to deal
17   -in the Software without restriction, including without limitation the rights
18   -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
19   -copies of the Software, and to permit persons to whom the Software is
20   -furnished to do so, subject to the following conditions:</p>
21   -
22   -<p>1) The above copyright notice and this permission notice shall be included in all
23   -copies or substantial portions of the Software.<p>
24   -
25   -<p>2) Appropriate credit must be given.
26   -
27   -<p>3) A link to the license must be provided, and indicate if changes were made. This may be done in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.</p>
28   -
29   -<p>THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
30   -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
31   -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
32   -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
33   -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
34   -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
35   -SOFTWARE.</p>
36   -
37   -</body>
38   -</html>
README.html
View file @d12d87d
... ... @@ -1,49 +0,0 @@
1   -<html>
2   -<body>
3   -
4   -<h1>###### RepTB README ######</h1>
5   -
6   -
7   -<h3>Usage</h3>
8   -
9   -python reptb_nbi.py inputfile.csv outputfile.csv
10   -
11   -
12   -<h3>Prerequisites:</h3>
13   -
14   -<ol>
15   -<li>This algorithm has been tested on Python 2.7</li>
16   -<li>The Python program needs following modules to be imported:</li>
17   -<ul> <li>numpy</li>
18   - <li>csv</li>
19   - <li>numpy.matlib</li></ul>
20   -
21   -
22   -</ol>
23   -<h3>Input File</h3>
24   -
25   -<p>/RepTB/inputfile.csv : This is the input file that we have used used in our study. This file contains the drug-target interactions from drugbank and GO mapping.</p>
26   -
27   -
28   -<h3>NBI Algorithm</h3>
29   -
30   -<p>/RepTB/reptb_nbi.py : The NBI code snippet contains comments that would help the researchers with their own data. All the researchers have to do is upload their GO mapped DTI file (inputfile.csv)and run the python code. The code will first generate an adjacent matrix using the input file and then create a prediction matrix called NBIscore which will be a m x n matrix. The output file (outputfile.csv) will be created which will contain predicted DTIs having scores within 20% of the max score for each Target.</p>
31   -
32   -<h3>Output File</h3>
33   -
34   -<p>/RepTB/outputfile.csv : This is the final output file generated using our input file and contains the prioritized list of predicted DTIs with the predicted scores. If you are uploading your own input file containing the DTIs, you might need to change the name of the output file in the python code provided.</p>
35   -
36   -
37   -<h3>Supporting Files:</h3>
38   -
39   -<ul><li>Generating_random_netoworks.m: This is a matlab file that was used to generate random networks with the same number of nodes but varying drug interactions and running through NBI. This file was only used to establish the robustness of the NBI.</li>
40   -
41   -<li>uniprot_go_annotations_mf_strong_evidence_new.csv: This file contains the mapping of the molecular function GO terms and Uniprot Ids.</li></ul>
42   -
43   -<h3>***Remarks***</h3>
44   -
45   -<p>Customised GO mapped input files can be fed into the NBI algorithm for different model systems.</p>
46   -
47   -
48   -</body>
49   -</html>
RepTB/LICENSE.html
Diff comments   View file @624f93a
... ... @@ -0,0 +1,25 @@
  1 +<!DOCTYPE html>
  2 +<html>
  3 +<body>
  4 +
  5 +
  6 +<h1>RepTB License</h1>
  7 +<div class="two columns alpha">
  8 +<img src="https://licensebuttons.net/l/by/3.0/88x31.png" alt="" width="88" height="31">
  9 +</div>
  10 +
  11 +
  12 +Copyright (c) 2018 Anshu Bhardwaj
  13 +
  14 +
  15 +<h3>You are free to:</h3>
  16 +<big>Share</big> : copy and redistribute the material in any medium or format
  17 +<big>Adapt</big> : remix, transform, and build upon the material for any purpose, even commercially.
  18 +
  19 +
  20 +<h3>Under the following terms:</h3>
  21 +<p><big>Attribution</big> : You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.</p>
  22 +
  23 +<p><big>No additional restrictions</big> : You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.</p>
  24 +</body>
  25 +</html>
... ...
RepTB/README.html
Diff comments   View file @624f93a
... ... @@ -0,0 +1,43 @@
  1 +<html>
  2 +<body>
  3 +
  4 +<h1>###### RepTB README ######</h1>
  5 +
  6 +
  7 +<h3>Usage</h3>
  8 +
  9 +python reptb_nbi.py inputfile.csv outputfile.csv
  10 +
  11 +
  12 +<h3>Prerequisites:</h3>
  13 +
  14 +<ol>
  15 +<li>This algorithm has been tested on Python 2.7</li>
  16 +<li>The Python program needs following modules to be imported:</li>
  17 +<ul> <li>numpy</li>
  18 + <li>csv</li>
  19 + <li>numpy.matlib</li></ul>
  20 +
  21 +
  22 +</ol>
  23 +<h3>Input File</h3>
  24 +
  25 +<p>inputfile.csv : This is the input file that we have used in our study. This file contains the drug-target interactions from drugbank and GO mapping. Customised GO mapped input files can be fed into the NBI algorithm for different model systems.</p>
  26 +
  27 +
  28 +<h3>NBI Algorithm</h3>
  29 +
  30 +<p>reptb_nbi.py : The NBI code snippet contains comments that would help the researchers with their own data. All the researchers have to do is upload their GO mapped DTI file (inputfile.csv)and run the python code. The code will first generate an adjacent matrix using the input file and then create a prediction matrix called NBIscore which will be a m x n matrix. The output file (outputfile.csv) will be created which will contain predicted DTIs having scores within 20% of the max score for each Target.</p>
  31 +
  32 +<h3>Output File</h3>
  33 +
  34 +<p>outputfile.csv : This is the final output file generated using the input file and contains the prioritized list of predicted DTIs with the predicted scores. If you are uploading your own input file containing the DTIs, you might need to change the name of the output file in the python code provided.</p>
  35 +
  36 +
  37 +<h3>Supporting Files:</h3>
  38 +
  39 +
  40 +<li>uniprot_go_annotations_mf_strong_evidence_new.csv: This file contains the mapping of the molecular function GO terms and Uniprot Ids.</li></ul>
  41 +
  42 +</body>
  43 +</html>
... ...