Many of todays scientists face the following problem: They need to integrate a substantial number of computational tools to solve problems.
SciCraft is a software designed to make software and method integration easier. It is also designed to make different computational tools easily available to the user. In theory SciCraft can be used to integrate any type of software, but we have in particular focused on the integration and availability of data analysis methods which originate from fields such as bioinformatics, statistics, chemometrics and artificial intelligence. One reason for this focus is that irrespective of the scientific field in question, there is almost always a need to perform data analysis.
The SciCraft Molecular Editor
SciCraft contains a powerful 3D molecular editor and visualization node.
In chemistry and biology there is a need to construct and display the 3D structure of molecules. There are many programs for this, however there is problem to integrate this functionality with e.g. data analysis tools. In e.g. quantitative structure-activity relationships (QSAR) we seek to construct models that are able to predict the activity of molecules from their structure. As the statistical models are investiated it is often necessary to combine the plotting of statistical results (such as e.g. score plots from principal component analysis) to the ability to view 3D structures of individual molecules. In techniques such as comparative field analysis (CoMFA) it is common to plot regression coefficients that can be interpreted as intensities at 3D localised points together with the 3D structure of an example molecule.
Microarray Analysis Tools
SciCraft provides tools for analysis through its use of Bioconductor functions.
Bioconductor is a large R package containing tools for bioinformatics. Of particular interest to us to create nodes in SciCraft based on Bioconductor functions related to analysis of microarrays. At the present only a small subset of all Bioconductor methods are connected to SciCraft, however it is expected that more functions will be made available in the near future.
SciCraft Also Runs R Programs
SciCraft allows people to run their R software as nodes
R is a powerful high level programming language used mainly in statistics. One of the main advantages with the R plugin for the users of SciCraft is the large number of advanced methods availble in this language.
On the R package page you can find a large number of statistical tools. In principle, any of these methods can be made available through SciCraft.
Run Your Matlab/Octave Software In SciCraft
Many nodes in SciCraft are actually Matlab or Octave programs running in the background
Matlab is perhaps one of the most commonly used high level languages used today for science and engineering. Many scientist have developed new data analysis and processing tools in this language which now can be made easily available through SciCraft. However, as Matlab is a commercial product and very expensive, SciCraft does use this to run Matlab m-files. For this we use Octave which is an open source Matlab clone. Since it is open source we can without problems bundle this with SciCraft to allow the users direct access to a large library of methods written in Matlab syntax.