Commit dc556378 authored by Luka Stanisic's avatar Luka Stanisic

rel2: updating documentation

parent 588897c6
......@@ -2,11 +2,12 @@
Authors of BioEM
=======================
*** v1.0 in 2016
*** v2.0 in 2017
Pilar Cossio
David Rohr
Fabio Barruffa
Luka Stanisic
Markus Rampp
Volker Lindenstruth
Gerhard Hummer
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@Article{Plancherel,

@Article{Plancherel,
Title = {{Contribution à l'étude de la représentation d'une fonction arbitraire par les intégrales définies}},
Author = {Plancherel, Michel and Mittag-Leffler},
Journal = {{Rendiconti del Circolo Matematico di Palermo}},
......@@ -1328,10 +1330,18 @@ Unique-ID = {{ISI:000185731300001}},
@article{BioEM_server,
title = "BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images",
journal = "Comput. Phys. Commun.",
author = "Cossio, Pilar and Rohr, David and Baruffa, Fabio, and Rampp, Markus and Lindenstruth, Volker and Hummer, Gerhard",
year = "2016"
author = "Cossio, Pilar and Rohr, David and Baruffa, Fabio and Rampp, Markus and Lindenstruth, Volker and Hummer, Gerhard",
year = "2017"
}
@article{BioEM_cring,
title = " Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase",
journal = "Submitted",
author = "Cossio, Pilar and Allegretti, Matteo and Mayer, Florian and Mueller, Volker and Vonck, Janet and Hummer, Gerhard",
year = "2017"
}
@article{CossioHummerJSB_2013,
title = "Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies ",
journal = "J. Struct. Biol.",
......
# BioEM: Bayesian inference of Electron Microscopy
# 1.0 VERSION: June, 2016
## Build status and test coverage
[![Build status](https://gitlab.mpcdf.mpg.de/sluka/BioEM/badges/master/build.svg)](https://gitlab.mpcdf.mpg.de/sluka/BioEM/commits/master)
[![Code coverage](https://gitlab.mpcdf.mpg.de/sluka/BioEM/badges/master/coverage.svg?job=total_coverage)](http://sluka.pages.mpcdf.de/BioEM/)
[![Doc]()]()
[![License: GPL v3][license-badge]](License.txt)
## Contributors
Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, Volker Lindenstruth and Gerhard Hummer
Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, Luka Stanisic, Volker Lindenstruth and Gerhard Hummer
## References
......@@ -28,18 +35,16 @@ For a detailed description of the BioEM software see the BioEM_Maunal.pdf that i
++++++++++++ FROM COMMAND LINE +++++++++++
Command line inputs:
--Modelfile arg (Mandatory) Name of model file
--Particlesfile arg if BioEM (Mandatory) Name of particle-image file
--Inputfile arg if BioEM (Mandatory) Name of input parameter file
--PrintBestCalMap arg (Optional) Only print best calculated map. NO BioEM (!)
--Modelfile arg (Mandatory) Name of model file
--Particlesfile arg (Mandatory) Name of particle-image file
--Inputfile arg (Mandatory) Name of input parameter file
--ReadOrientation arg (Optional) Read file name containing orientations
--ReadPDB (Optional) If reading model file in PDB format
--ReadMRC (Optional) If reading particle file in MRC format
--ReadMultipleMRC (Optional) If reading Multiple MRCs
--DumpMaps (Optional) Dump maps after they were read from
particle-image file
--DumpMaps (Optional) Dump maps after they were read from particle-image file
--LoadMapDump (Optional) Read Maps from dump option
--OutputFile arg (Optional) For changing the outputfile name
--OutputFile arg (Optional) For changing the outputfile name
--help (Optional) Produce help message
Details for the inputfiles and formats are provided in chapters 1 and 2 of the BioEM_Manual.pdf.
......@@ -97,10 +102,6 @@ Dependencies and software requirements:
for free software see: http://www.fftw.org
* BOOST
for free software see: http://www.boost.org/
* CUDA (required to build and run the GPU version)
for free software see: https://developer.nvidia.com/cuda-downloads
......@@ -118,3 +119,5 @@ threads etc. These are passed via environment variables. See chapter 3 of the Bi
The BioEM program is a free software, under the terms of the GNU General Public License as published by the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful, but without any warranty. See License.txt for more details.
[license-badge]: https://img.shields.io/badge/License-GPL%20v3-blue.svg
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