Working in the underground to keep the data coming.
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underdarkgo

README.md

Underdark Go

If you use this code or application, please cite the original paper published by Bioinformatics: 10.1093/bioinformatics/btx760

Underdark Go

For a complete overview and detailed installation instructions for this project, please visit the project website.

Getting Started

The easiest way to get started with Underdark Go is pulling and running the docker image.

docker run -d -p 80:8081 -v /your/host/dir:/underdarkgo/data --name underdark daenuprobst/underdark-go

Underdark Go exposes port 8081 by default. Depending on your network settings and topology you might want to change this using the -p argument (see example above). The directory /underdarkgo/data has to be mounted to a host directory (/your/host/dir in the example above) where a configuration file config.json describes the data within a sub-directory.

Configuration

The file config.json stores four levels of meta-data on the data to be provided via the service.

  1. Database information
  2. Fingerprint information
  3. Variant information
  4. Map information

These levels also reflect the directory tree in which the files containing the data are stored. The configuration file config.json has the following format

{
    "databases": [
        {
            "id": "acmebase-2",
            "name": "ACMEbase Version 2.0",
            "description": "A database that contains everything.",
            "directory": "acmebase2",
            "fingerprints": [
                {
                    "id": "xfp",
                    "name": "Xfp",
                    "description": "The Xfp fingerprint.",
                    "directory": "Xfp",
                    "infosFile": "acmebase2.xfp.info",
                    "infoIndicesFile": "acmebase2.xfp.info.index",
                    "variants": [
                        {
                            "id": "250",
                            "name": "Low Resolution",
                            "description": "Binned with a resolution of 250 x 250 x 250.",
                            "resolution": 250,
                            "dataTypes": [
                                "uint16",
                                "uint16",
                                "uint16"
                            ],
                            "directory": "250",
                            "indicesFile": "acmebase2.xfp.250.dat",
                            "coordinatesFile": "acmebase2.xfp.250.xyz",
                            "maps": [
                                {
                                    "id": "hac",
                                    "name": "Heavy Atom Count",
                                    "description": "The number of heavy (non-hydrogen) atoms in the molecule.",
                                    "mapFile": "acmebase2.xfp.250.1.map",
                                    "dataTypes": [
                                        "float32",
                                        "float32",
                                        "float32"
                                    ]
                                },
                                ...
                            ]
                        },
                        ...
                    ]
                },
                ...
            ]
        }
    ]
}

The directory structure of the above example would thus look like this

.
+-- config.json
+-- acmebase2
    +-- Xfp
        |-- acmebase2.xfp.info
        |-- acmebase2.xfp.info.index
        +-- 250
            |-- acmebase2.xfp.250.dat
            |-- acmebase2.xfp.250.xyz
            |-- acmebase2.xfp.250.1.map

All files can be generated from initial files containing one molecular fingerprint (of any type) per line. Python 3.x scripts as well as a bash script for automation can be found here. This repository also contains a dockerized flask based project to enable the PCA projection of additional molecular fingerprints using the models generated for the initial data set.

Build

Download Go

Install Go

sudo tar -xvf gox.y.linux-amd64.tar.gz
sudo mv go /usr/local

Create a directory where built Go executables will be stored

mkdir ~/go
mkdir ~/go/bin

Edit ~/.profile by adding (at the end)

export PATH=$PATH:/usr/local/go/bin
export GOPATH=/usr/local/go/bin
export GOBIN=$HOME/go/bin
# GOBIN is set to the directory created in the previous step

Update profile

source ~/.profile

Get the socket.io package

go get github.com/gorilla/websocket

You can the build the project

go build -o underdarkgo main.go