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README
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Program: Vini in silico model of cancer, version 4.0
Description: Vini is in silico model of cancer. It can be used for the pathway-based virtual drug screening, or for testing various hypothesis related to cancer.
The development team: Drasko Tomic, Josip Mesaric
Licensing:
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Vini code is free to download and use. It is distributed under GNU General Public License v3.0 (GNU GPLv3). This license is in COPYING file. However, Vini also uses other programs and databes, like Autodock Vina, ADFR, MGL Tools, Chimera, Rosetta, Drugbank, COSMIC, KEGG, and SWISS-MODEL, that request license agreement. They are free to use for academic purpouses.
Hardware & OS requirements:
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Vini is the supercomputing applications and needs at least 10 cluster nodes to run smoothly.
For the prediction of protein structures, Vini offers a choice between two tools: AlphaFold and Swiss-Model. If AlphaFold is used, predictions can run in parallel, provided that the minimum memory size of each computing node is 128GB. Swiss-Model does not have such a limitation because the predictions are done on an external server. However, predictions are then executed sequentially, one by one.
Vini has been tested on RHEL 7, and CENTOS 7 and 8. The supported workload manager is SLURM.
Registering for third party programs and external databases/services:
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Vini uses third party programs and data from external databes and services. Registration for some of them is needed before running Vini. This registrations are free for academic institutions and approvals are tipically received within one hour or less.
It is strongly recommended that all registrations be done before starting Vini. Registration links:
Drugbank: https://go.drugbank.com/public_users/sign_up and register
Cosmic: https://cancer.sanger.ac.uk/cosmic/register and register
Swiss-Model: https://swissmodel.expasy.org/, pick <create account> in the right uper corner and register
Chimera: https://www.cgl.ucsf.edu/cgi-bin/chimera_registration.py and register
Rosetta: https://els2.comotion.uw.edu/product/rosetta
Installing and running Vini:
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Download code from Git: git clone https://github.com/draskot/Vini
Start Vini (sh Vini) and follow the instructions.