DENSSWeb is a web frontend for the DENSS algorithm. DENsity from Solution Scattering (DENSS) is an algorithm used for calculating ab initio electron density maps directly from solution scattering data. DENSSWeb provides a web based frontend interface allowing users to run complex DENSS pipelines and view results in a browser. DENSSWeb performs parallel DENSS runs and the resulting density map is displayed using a custom LiteMol plugin along with a plot of the fourier shell correlation (FSC) curve.
A demo fo DENSSWeb can be found here.
DENSSWeb can be run locally on a single machine or on multiple machines in a clustered environment. DENSSWeb consists of a server and client worker. The server runs an embedded web server and the client worker runs the DENSS pipeline.
A web browser with WebGL support. To check if your browser supports WebGL see here.
Install all required software (see Required Software section). Download the current release of DENSSWeb for your platform here.
Unpack the DENSSWeb release:
$ tar xzvf denssweb-VERSION-OS-amd64.tar.gz $ cd denssweb-VERSION-OS-amd64
Create the config file and edit the paths to required software:
$ cp denssweb.yaml.sample denssweb.yaml (edit to taste)
Start the DENSSWeb client/server:
$ ./denssweb -d run
Point your browser at http://localhost:8080 and submit a Job
To limit the number of threads DENSSWeb spawns use the -t option.
By default, this will be set to the number of cores available on your machine.
For example:
$ ./denssweb -d run -t 4
The raw output files for each job are stored in work_dir/denss-JOBID.
work_dir by default is set to a directory named denssweb-work in your
current working directory but you can override this in the denssweb.yaml file.
The complete log file for a job is in a file named denss-JOBID.log.
If you're running DENSSWeb on a server you must edit the bind and
base_url settings accordingly.
DENSSWeb is written in Go and requires go v1.11 or greater. To compile from source run:
$ git clone --recursive https://github.com/ubccr/denssweb $ cd denssweb $ go build . $ cp denssweb.yaml.sample denssweb.yaml (edit to taste) templates: "dist/templates"
Next, compile the DENSS Viewer LiteMol plugin. For instructions see here
Assemble the web assets and template files:
$ ./build.sh tmpl
Run denssweb:
$ ./denssweb -d run
The following guide assumes you're running Linux Ubuntu 18.04. You will need to adjust package names for your distro.
Install required packages:
$ apt-get install libhdf5-100 libhdf5-dev libpng-dev libtiff5 libtiff5-dev \
python-qt4 python-qt4-gl python-opengl python-matplotlib libfftw3-3 libfftw3-dev \
libgsl-dev db-util libdb-dev python-bsddb3 libboost-all-dev python-dev cmake \
cmake-curses-gui ipython libgl1-mesa-dev libglu1-mesa-dev libftgl2 libftgl-dev
python-scipy build-essential git python-numpy
Clone and install DENSS:
$ git clone https://github.com/tdgrant1/denss $ cd denss $ python setup.py install
DENSSWeb is released under the GPLv3 license. See the LICENSE file.