Template:EM software tool

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This is a template to list a software tool for the Wikibook Software Tools For Molecular Microscopy.

see Template:Infobox software for more options

required fields[edit]

  • name: short name of the software tool
  • full name: full name of the software tool
  • website: link to web page of software tool
  • short description: single sentence description of software tool
  • long description: paragraph description of software tool
  • initial release
  • version: current version of software
  • contact: contact email for the project
  • os support: e.g., MacOS9, VMS
  • program language
  • image support
  • cost:
  • open source:
  • references:

Common open source licenses[edit]

see w:Comparison_of_free_software_licenses for a detailed list

Notes: The GPL is usually considered the most restrictive, meaning that any derivative works must also be open source. GLPL and BSD allow one to incorporate you code into a closed source for-profit program. A prominent example is the BSD licensed w:Webkit is used in the closed source w:Apple Safari.

empty template[edit]

{{EM software tool
|name=
|website=
|long description=
|version=
|contact=
|os support=
|image support=
|cost=
|license=
|program language=
|ref1={{Cite journal
  |first1=
  |last1=
  |coauthors=
  |year=
  |title=
  |journal=
  |volume=
  |issue=
  |pages=
  |pmid=
  |doi=
  |pmcid=
}}
}}

Here is a good tools for filling out the Cite journal field: Wikipedia template filling

example[edit]

{{EM software tool
|name=Bsoft
|website=http://bsoft.ws
|long description=Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. Several workflows such as for single particle analysis and tomography are supported with parameter exchange as well as the ability to do distributed processing across heterogeneous clusters of computers. Several tools are available for modeling structures as atomic coordinates or larger scale models for the interpretation of large molecular complexes such as viruses and sub-cellular organelles.
|version=1.6.0
|contact=Bernard_Heymann at nih.gov
|os support=Unix (Mac OS X, IRIX, Linux, AIX, Solaris, Tru64), VMS
|image support=BioRad, Brix, CCP4, Digital Instruments, Digital Micrograph, EM, Goodford, GRD, Imagic, JPEG, MFF, Image Magick, MRC, PIC, PIF, PNG, Spider, Suprim, TIFF, RAW
|cost=Free
|open source={{Yes}}
|ref1={{Cite journal|first1=J.B.|last1=Heymann| year=2001|title=Bsoft: image and molecular processing in electron microscopy| journal=Journal of Structural Biology|volume=133|issue=2-3|pages=156-69}}
|ref2={{Cite journal|first1=J.B.|last1=Heymann| first2=D.M.|last2=Belnap| year=2007|title=Bsoft: Image processing and molecular modeling for electron microscopy| journal=Journal of Structural Biology|volume=157|pages=3-18}}
|ref3={{Cite journal|first1=J.B.|last1=Heymann| first2=G.|last2=Cardone| first3=D.C.|last3=Winkler| first4=A.C.|last4=Steven| year=2008|title=Computational resources for cryo-electron tomography in Bsoft| journal=Journal of Structural Biology|volume=161|pages=232-242}}
}}

produces:


Bsoft[edit]

  • Website: http://bsoft.ws
  • Current version: 1.6.0
  • Contact: Bernard_Heymann at nih.gov
Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. Several workflows such as for single particle analysis and tomography are supported with parameter exchange as well as the ability to do distributed processing across heterogeneous clusters of computers. Several tools are available for modeling structures as atomic coordinates or larger scale models for the interpretation of large molecular complexes such as viruses and sub-cellular organelles.
  • Support: Operating systems: Unix (Mac OS X, IRIX, Linux, AIX, Solaris, Tru64), VMS Image format support: BioRad, Brix, CCP4, Digital Instruments, Digital Micrograph, EM, Goodford, GRD, Imagic, JPEG, MFF, Image Magick, MRC, PIC, PIF, PNG, Spider, Suprim, TIFF, RAW
  • Cost: Free
  • Primary Publication to Cite:
    • Heymann, J.B. (2001). "Bsoft: image and molecular processing in electron microscopy". Journal of Structural Biology 133 (2-3): 156-69. 
  • Additional References:
    • Heymann, J.B.; Belnap, D.M. (2007). "Bsoft: Image processing and molecular modeling for electron microscopy". Journal of Structural Biology 157: 3-18. 
    • Heymann, J.B.; Cardone, G.; Winkler, D.C.; Steven, A.C. (2008). "Computational resources for cryo-electron tomography in Bsoft". Journal of Structural Biology 161: 232-242.