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# App EBAME-2022 Metabolic network reconstruction and modelling
Integration of tools for metabolic network reconstruction and metabolling modelling for the EBAME-2023 school.
## Description
**[8th EBAME Workshop on Computational Microbial Ecogenomics](https://maignienlab.gitlab.io/ebame8)**
Microbial Ecology is undergoing rapid evolution and dramatic progresses thanks to the combined advances of next-generation DNA sequencing technologies and computational approaches for data analysis and visualization. As a result,"microbial ecogenomics" has become an essential part of investigations of marine or terrestrial habitats, or host-microbe interactions. The aim of the EBAME workshop is to bring together researchers who generate complex 'omics datasets to investigate biologically ecological and evolutionnary questions with researchers who develop new concepts and computational methods to analyze such datasets.
**Tutorial on metabolic network reconstruction and modelling**
For this session we will learn to reconstruct, explore and simulation metabolic networks at the scales of the species and of the community.
**Guide**
Once the VM is up, you can connect with SSH, and follow the [tutorial](https://gitlab.inria.fr/cfrioux/ebame)
```
ssh ubuntu@<your.vm.ip.address>
```
The reference data are availabe in the directory `/ifb/data/public/teachdata/ebame-2022/metator/` only on the VM created on the `ifb-core-cloudbis`site. #TODO
## Tools
* Tools : Ubuntu 22.04 #TODO
* [Bowtie2](https://biosphere.france-bioinformatique.fr/catalogue/tool/40/)
* [CheckM](https://biosphere.france-bioinformatique.fr/catalogue/tool/314/)
* [hicstuff](https://biosphere.france-bioinformatique.fr/catalogue/tool/316/)
* [MetaTOR](https://biosphere.france-bioinformatique.fr/catalogue/tool/313/)
* [Pairix](https://biosphere.france-bioinformatique.fr/catalogue/tool/315/)
* [SAMtools](https://biosphere.france-bioinformatique.fr/catalogue/tool/116/)
## Topics
* Microbial Ecology
* Metabolic Modelling
* Metabolic Networks
* Metagenomics
## Contact
* Clémence Frioux (Inria)
## Developpers
* [Clémence Frioux](https://cfrioux.github.io/) (Inria)
#!/bin/bash
# This script is executed on the virtual machine during the Installation phase (need to be ran as root!).
# It is used to record a predefined VM-image of the appliance.
# Otherwise executed first during a cloud deployement in IFB-Biosphere
source /etc/profile
APP_CONFIG_URL1=https://gitlab.inria.fr/cfrioux/ebame/-/raw/main/conda/ebame_metabo_gapseq.yml?ref_type=heads
APP_CONFIG_URL2=https://gitlab.inria.fr/cfrioux/ebame/-/raw/main/conda/ebame_metabo_reasoning.yml?ref_type=heads
APP_DIR=/ifb/arch/metabo
# APP_CONFIG_FILE=$APP_DIR/metator.yaml
# git clone https://github.com/koszullab/metaTOR.git ${APP_DIR}
APP_CONFIG_FILE1=$APP_DIR/ebame_metabo_gapseq.yml
APP_CONFIG_FILE2=$APP_DIR/ebame_metabo_reasoning.yml
mkdir -p $APP_DIR
curl -LJ "$APP_CONFIG_URL1" -o $APP_CONFIG_FILE1
curl -LJ "$APP_CONFIG_URL2" -o $APP_CONFIG_FILE2
conda env create -f $APP_CONFIG_FILE1
conda env create -f $APP_CONFIG_FILE2
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