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توضیحات

Single Particle Data Analysis Suite

ویژگی	مقدار
سیستم عامل	-
نام فایل	arachnid-0.1.7
نام	arachnid
نسخه کتابخانه	0.1.7
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Robert Langlois
ایمیل نویسنده	rl2528@columbia.edu
آدرس صفحه اصلی	http://www.arachnid.us
آدرس اینترنتی	https://pypi.org/project/arachnid/
مجوز	GPL

Arachnid ======== Arachnid 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 Prime A 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. #. pySPIDER This 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 selection - ViCer: Automated unsupervised particle verification This software is under development by the `Frank Lab`_ and is licensed under `GPL 2.0 <http://www.arachnid.us/license.html>`_ or later. For more information, see `http://www.arachnid.us <http://www.arachnid.us>`_. Alternatively, HTML documentation can be built locally using `python setup.py build_sphinx`, which assumes you have the prerequisite Python libraries. The documents can be found in `build/sphinx/html/`. How to cite =========== The main reference to cite is: Langlois, R. E., Ho D. N., Frank, J., 2014. Arachnid: Automated Image-processing for Electron Microscopy. In Preparation. See `CITE <http://www.arachnid.us/CITE.html>`_ for more information and downloadable citations. Important links =============== - Official source code repo: https://github.com/ezralanglois/arachnid - HTML documentation (stable release): http://www.arachnid.us/ - Download releases: https://binstar.org/ - Issue tracker: https://github.com/ezralanglois/arachnid/issues - Mailing list: http://groups.google.com/group/arachnid-general - Cite: http://www.arachnid.us/CITE.html Dependencies ============ The 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`_. Install ======= The 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 arachnid Alternatives: # 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 -c https://conda.binstar.org/ezralanglois arachnid Development =========== You can check out the latest source with the command:: git clone https://github.com/ezralanglois/arachnid/arachnid.git .. _`Frank Lab`: http://franklab.cpmc.columbia.edu/franklab/ .. _`Anaconda`: https://store.continuum.io/

نحوه نصب

نصب پکیج whl arachnid-0.1.7:

pip install arachnid-0.1.7.whl

نصب پکیج tar.gz arachnid-0.1.7:

pip install arachnid-0.1.7.tar.gz