TB-Drugome - Run 126

Published: 9 September 2016| Version 1 | DOI: 10.17632/r69mvkckmn.1
Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Philip E. Bourne


A run of the TB-Drugome Workflow.


Steps to reproduce

The TB-Drugome Workflow is complicated to use without the proper knowledge in bioniformatics and computer science. This section aims to provide the initial pointers and references to look at when trying to reuse the TB-Drugome workflow. - It is recommended to first understand the flow of the data by looking at published run schema. - Then look at the original Drugome paper for further information and the tools being used. - Once you are familiar with the workflow, have a look at the published workflow run, decompose the workflow in the different modules and test them separately. - In order to test the different steps of the workflow, you can access http://wind.isi.edu/marbles/ and import the "Drugome" domain. Different workflows already encode the sub parts of the workflow and are ready to be run. Note that you will need to ask for a user and password (contact Yolanda Gil, Varun Ratnakar or Daniel Garijo). - You will find suitable inputs to test the workflow in the input data section of this document. If you reuse the inputs, the outputs should look like the ones described here. - If you want to reuse the workflow with other data it is very important to follow the format of the input files. If you have any problem with any software in particular, check our detailed timeline. We may have experienced your problems before! - Are you stuck at some point of the workflow? Do you have problems accessing some data? Please contact me and I will be happy to help you.


University of California San Diego


Computational Method