IEDB scipion plugin

Documentation under development, sorry for the inconvenience

Scipion framework plugin for the use of tools provided by IEDB epitope tools. This plugin allows to use programs from the IEDB website for B-cell, MHC-I, MHC-II epitope predictions and population coverage within the Scipion framework. You need to download the IEDB files before installing the plugin, see section "Download IEDB files" for details.

Download IEDB files

IEDB contains several software packages for epitope prediction and other tools meant for academic use only. You can download these packages in http://tools.iedb.org/tepitool/download/ . Now, specific instructions for each of the packages will be provided.

1. B-cell epitope prediction

Antibody Epitope Prediction tool contains collection of python scripts, specific binary for BepiPred and a pickled file containing residue scales for different methods. The zip file can be downloaded from https://services.healthtech.dtu.dk/cgi-bin/sw_request?software=bepipred&version=3.0&packageversion=3.0b&platform=src

Once you obtain the software file (a zip) you have several options to help Scipion finding it:

Option 1) Edit the scipion.conf file and add the variable: BEPIPRED_ZIP = <PathToBepiPredZip>. This way, Scipion will unzip and move the corresponding files to the scipion/software/em folder and install BepiPred.

Option 2) If you have unzipped BepiPred yourself you can either:

2.1) Move the folder (of the form BepiPred3_src) to the scipion/software/em folder. Scipion will find it there.

2.2) Specify the location of the BepiPred folder in the scipion.conf file as: BEPIPRED_HOME = <PathToBepiPred3_src>

Option 3) If you have already installed BepiPred (creating the python environment needed), you need to specify Scipion in the scipion.conf file both:

3.a) The path to the BepiPred folder as: BEPIPRED_HOME = <PathToBepiPred3_src> and

3.b) The activation command as: BEPIPRED_ACTIVATION_CMD = <ActivationCommand>

This way, Scipion will use your own BepiPred installation.

2. MHC-I epitope prediction

The MHC_I binding tool contains a collection of following peptide binding prediction methods for Major Histocompatibility Complex (MHC) class I molecules.The collection is a mixture of pythons scripts and linux 32-bit environment specific binaries. The tar file can be downloaded from http://tools.iedb.org/mhci/download/

Once you obtain the software file (a tar.gz) you have several options to help Scipion finding it:

Option 1) Edit the scipion.conf file and add the variables:

• MHC-I_TAR = <PathToMhc-ITar> (IEDB_MHC_I-3.1.5.tar.gz)

This way, Scipion will untar and move the corresponding files to the scipion/software/em folder and install mhc-i.

Option 2) If you have unzipped the mhc-i tars yourself you can either:

2.1) Move the folder (of the form mhc_i) to the scipion/software/em folder. Scipion will find it there.

2.2) Specify the location of the MHC folder in the scipion.conf file as: MHC-I_HOME = <PathToMhc-I_folder>

3. MHC-II epitope prediction

The MHC_II binding tool contains a collection of following peptide binding prediction methods for Major Histocompatibility Complex (MHC) class II molecules.The collection is a mixture of pythons scripts and linux 32-bit environment specific binaries. The tar file can be downloaded from http://tools.iedb.org/mhcii/download/

Once you obtain the software file (a tar.gz) you have several options to help Scipion finding it:

Option 1) Edit the scipion.conf file and add the variables:

• MHC-II_TAR = <PathToMhc-IITar> (IEDB_MHC_II-3.1.5.tar.gz)

This way, Scipion will untar and move the corresponding files to the scipion/software/em folder and install mhc-ii.

Option 2) If you have unzipped the mhc-ii tars yourself you can either:

2.1) Move the folder (of the form mhc_ii) to the scipion/software/em folder. Scipion will find it there.

2.2) Specify the location of the MHC folder in the scipion.conf file as: MHC-II_HOME = <PathToMhc-II_folder>

4. Population coverage tool

Population Coverage tool contains collection of python scripts, a 'deps' directory as required/dependency, which includes a pickled file containing all population coverage data (various population, alleles and frequencies) and necessary python scripts. The tar file can be downloaded from http://tools.iedb.org/population/download/

Once you obtain the software file (a tar.gz) you have several options to help Scipion finding it:

Option 1) Edit the scipion.conf file and add the variables:

• COVERAGE_TAR = <PathToPopCoverageTar> (IEDB_Population_Coverage-3.0.2.tar.gz)

This way, Scipion will untar and move the corresponding files to the scipion/software/em folder and install mhc-ii.

Option 2) If you have unzipped the population_coverage tars yourself you can either:

2.1) Move the folder (of the form population_coverage) to the scipion/software/em folder. Scipion will find it there.

2.2) Specify the location of the MHC folder in the scipion.conf file as: COVERAGE_HOME = <PathToPopCoverage_folder>

Install this plugin

You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

• Stable version

scipion installp -p scipion-chem-iedb

OR

• through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

• Developer's version

1. Download repository:

git clone https://github.com/scipion-chem/scipion-chem-iedb.git

2. Switch to the desired branch (main or devel):

Scipion-chem-iedb is constantly under development. If you want a relatively older an more stable version, use main branch (default). If you want the latest changes and developments, user devel branch.

cd scipion-chem-iedb
git checkout devel

3. Install:

scipion installp -p path_to_scipion-chem-iedb --devel

• Tests

To check the installation, simply run the following Scipion test:

Buildbot status

Status devel version:

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