Package: arachnid
ArachnidArachnid is an open source software package written primarily in Python that processes
images of macromolecules captured by cryo-electron microscopy (cryo-EM). Arachnid is
focused on automating the single-particle reconstruction workflow and can be thought
of as two subpackages:Arachnid PrimeA SciPy Toolkit (SciKit) that focuses on every step of the single-particle
reconstruction workflow up to orientation assignment and classification. This
toolkit also includes a set of application scripts and a workflow manager.pySPIDERThis subpackage functions as an interface to the SPIDER package. It includes
both a library of SPIDER commands and a set of application scripts to run
a set of procedures for every step of single-particle reconstruction including
orientation assignment but not classification.Arachnid Prime currently focuses on automating the pre-processing of the image
data captured by cryo-EM. For example, Arachnid has the following highlighted applications
handle the particle-picking problem:AutoPicker: Automated reference-free particle selectionViCer: Automated unsupervised particle verificationThis software is under development by theFrank Laband is licensed underGPL 2.0or later.For more information, seehttp://www.arachnid.us.Alternatively, HTML documentation can be built locally usingpython setup.py build_sphinx, which assumes you have the prerequisite
Python libraries. The documents can be found inbuild/sphinx/html/.How to citeThe main reference to cite is:Langlois, R. E., Ho D. N., Frank, J., 2014. Arachnid: Automated
Image-processing for Electron Microscopy. In Preparation.SeeCITEfor more information and downloadable citations.Important linksOfficial source code repo:https://github.com/ezralanglois/arachnidHTML documentation (stable release):http://www.arachnid.us/Download releases:https://binstar.org/Issue tracker:https://github.com/ezralanglois/arachnid/issuesMailing list:http://groups.google.com/group/arachnid-generalCite:http://www.arachnid.us/CITE.htmlDependenciesThe required dependencies to build the software are Python >= 2.6,
setuptools, Numpy >= 1.3, SciPy >= 0.7, matplotlib>=1.1.0, mpi4py>=1.2.2,
scikit-learn, scikit-image, psutil, sqlalchemy, mysql-python, PIL, basemap,
FFTW3 or MKL, and both C/C++ and Fortran compilers.It is also recommended you install NumPy and SciPy with an optimized Blas
library such as MKL, ACML, ATLAS or GOTOBlas.To build the documentation, Sphinx>=1.0.4 is required.All of these dependencies can be found in a single free binary
package:Anaconda.InstallThe prefered method of installation is to use Anaconda:# If you do not have Anaconda then run the following (assumes bash shell)

wget http://repo.continuum.io/miniconda/Miniconda-3.0.0-Linux-x86_64.sh
sh Miniconda-3.0.0-Linux-x86_64.sh -b -p $PWD/anaconda
export PATH=$PWD/anaconda/bin:$PATH

# If you have anaconda or just installed it, then run

conda install -c https://conda.binstar.org/ezralanglois arachnidAlternatives:# Install from downloaded source$ python setup.py install –prefix=$HOME# Using Setup tools$ easy_install arachnid# Using PIP$ pip install arachnid# Using Anaconda$ conda install -chttps://conda.binstar.org/ezralangloisarachnidDevelopmentYou can check out the latest source with the command:git clone https://github.com/ezralanglois/arachnid/arachnid.git