Difference between revisions of "Gnuplot"

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(Created page with "http://www.ks.uiuc.edu/Research/vmd/ VMD "is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemb...")
 
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[[http://www.ks.uiuc.edu/Research/vmd/ VMD]] "is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer."
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[[http://gnuplot.info Gnuplot]] "is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986."
  
  
 
====Type of Data====
 
====Type of Data====
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One respondent reported using all types of data with gnuplot.
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Unsurprisingly, most respondents use this software for molecular/atomic/protein visualisation.
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Others were more selective.
  
 
====Size of Data Set====
 
====Size of Data Set====
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Again, one respondent reported using any size of input. Another reported using 100s.
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This varies widely. About half the respondents have data sets smaller than a few GB. Two had data sets of 40 and 50 GB. Otherwise they had 1,000 or 30,000 atoms.
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====Advantages====
 
====Advantages====
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Advantages are hinted at in the text quoted above, taken from gnuplot's home page: it is open source, flexible and mature.
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The most widely cited advantages are
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*quality of output
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*range of supported file types
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*simple to use/script
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====Quality of Documentation/Tutorials====
 
====Quality of Documentation/Tutorials====
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Documentation is reported to be good, although less so for advanced features. Because it is such a well-established tool, extensive online tutorial material is available.
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Documentation was almost universally regarded as good or very good. One respondent stated it was difficult to navigate.
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====Range of Data Formats====
 
====Range of Data Formats====
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Huge flexibility, ranging from csv files to latex.
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Again, almost universally regarded as good, with two exceptions:
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*"temperamental with periodic images"
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*"no support for cif"
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====Level of Support Available====
 
====Level of Support Available====
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See above - extensive community support is available.
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A range of resources is used: mailing lists and online forum.
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====Performance====
 
====Performance====
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Is assessed as being "good".
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Performance generally regarded as good, especially on a desktop machine.
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====Limitations====
 
====Limitations====
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Input is by a scripting language that isn't to everyone's taste.
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*"Needs a good graphics card"
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*"TCL scripting is limited"
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*"Slow to load large data sets"
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*"Some additional analysis tools are unstable"
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*"Some representations not appropriate for periodic boundary conditions"
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*"Cannot interpret bond types"
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====Comments====
 
====Comments====
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Comments reiterated statements made earlier, the package is open source and free.
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The tools are free and open source
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Latest revision as of 13:27, 24 November 2014

[Gnuplot] "is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave. Gnuplot has been supported and under active development since 1986."


Type of Data

One respondent reported using all types of data with gnuplot. Others were more selective.

Size of Data Set

Again, one respondent reported using any size of input. Another reported using 100s.

Advantages

Advantages are hinted at in the text quoted above, taken from gnuplot's home page: it is open source, flexible and mature.

Quality of Documentation/Tutorials

Documentation is reported to be good, although less so for advanced features. Because it is such a well-established tool, extensive online tutorial material is available.

Range of Data Formats

Huge flexibility, ranging from csv files to latex.

Level of Support Available

See above - extensive community support is available.

Performance

Is assessed as being "good".

Limitations

Input is by a scripting language that isn't to everyone's taste.

Comments

Comments reiterated statements made earlier, the package is open source and free.

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