Subsections
SciCraft have 76 different nodes which are divided into 6 categories;
file, input , plot, toolboxes, tools and view. Each of the function
nodes in toolboxes, which are linked up with the plug-ins in contrib and core
makes use of an external program when they run.
These nodes (table 3.2 and 3.3) are capable of
reading and writing plug-in specific files.
File type support
Table 3.1:
File type support
Input node | Output node |
Matlab | R |
BASE | Molecule(PDB) |
Octave | Octave |
R | |
Molecule(PDB) | |
Textfile | |
GaussDal | |
Experiment | |
| |
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Table 3.2:
Summary of the InputNode.
Name | InputNode |
Category | FileHandler |
Description | Node that reads data from a file. |
Usage | This node is used for retrieving data from a file into a Module Diagram. A file is read and
the content in this file is parsed into data which can be used by SciCraft. |
Parameters | Filename |
Input ports | None |
Output ports | One port for each variable in the current file will be added. |
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Table 3.3:
Summary of the OutputNode.
Name | OutputNode |
Category | Filehandlers |
Description | Node that writes data to a file. |
Usage | This node is used for writing results calculated by SciCraft to a
file. Only file formats supported by SciCraft can be written. |
Parameters | Filename |
Input ports | One port for each variable that will be written to the file. |
Output ports | None |
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These nodes (table 3.4 and 3.5) are capable of
reading input commands for SciCraft.
Table 3.4:
Summary of the ParamNode.
Name | Param |
Category | Input |
Description | Node that reads commands from the user. |
Usage | This node is used for sending commands to SciCraft. |
Parameters | Command |
Input ports | None |
Output ports | Data |
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Table 3.5:
Summary of the UserQuery.
Name | UserQuery |
Category | Input |
Description | Node that reads queries from the user. |
Usage | Use this node to query the system. |
Parameters | Command |
Input ports | None. |
Output ports | Data |
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Nodes capable of showing plots based on data in SciCraft. These nodes are summed
up in (table 3.6 and 3.7) and a detailed coverage of plotting is given
in section
.
Table 3.6:
Summary of the Plot nodes.
Name | PlotNode |
Category | Plot |
Description | Node that is used to make plot based on calculated data in the
Module Diagram. |
Usage | This node's task is to show plots bases on data coming in on the
plotnode. In later edition of SciCraft it will be possible to select elements in
the plot and then send the data and a command to an edit node to remove these
elements from the dataset. |
Parameters | None |
Input ports | Arbitrarily many ports with input matrices |
Output ports | In later editions there will be one exit ports where a command
string is set. These ports will then be connected with an edit node which will
process the current dataset. |
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Table 3.7:
Summary of the DevelPlot nodes.
Name | DevelPlot |
Category | Plot |
Description | PlotNode under development. Better plots, but less functionallity. |
Usage | This node's task is to show plots bases on data coming in on the
userplot node. |
Parameters | None |
Input ports | Arbitrarily many ports with input matrices |
Output ports | In later editions there will be one exit ports where a command
string is set. These ports will then be connected with an edit node which will
process the current dataset. |
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Plugin nodes which executes different functions in an external
program, e.g. Octave or R.
Table 3.8:
Summary of the Function nodes.
Name | FunctionNode |
Category | None |
Description | Node responsible for communication with external programs. |
Usage | This node is used for communication with external programs. SciCraft
contains scripts which are used to generate different function nodes. These
nodes will then use these scripts to process data through the external
program. |
Parameters | Depending on the type of script the node contains. None of these
are meant to be edited by the user. |
Input ports | One port for each variable needed by the script this node will
execute. |
Output ports | One port for each data element generated by the external
program. |
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The node performs k-means cluster analysis. Table 3.9 gives a summary of the Kmeansc node.
Table 3.9:
Summary of the Kmeansc node.
Name | Kmeansc |
Category | Contrib/Classification |
Description | Node performs k-means cluster analysis. |
Usage | Add input matrix, number of clusters to search for, and maximum number of iterations. |
Parameters | Command |
Input ports | Input matrix, numbers of clusters and max iterations. |
Output ports | An exit port with CNT/R object with cluster centers. |
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The node performs k-nearest neighbour classification. Table 3.10 gives a summary of
the Knn2 node.
Table 3.10:
Summary of the Knn2 node.
Name | Knn2 |
Category | Contrib/Classification |
Description | Node performs k-Nearest neighbour classification. |
Usage | Add data matrix as the independent variables for the calibration samples. Add a vector containing the
classes for the samples given in the matrix. A value for the number of neighbours considered. An optinal matrix with a set of
test cases can be added. . |
Parameters | Command |
Input ports | Input matrix, A vector containing classes, number of neighbours, test matrix. |
Output ports | Percentwise calibration error, prediction error and predicted classes. |
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The node performs linear discriminant analysis. Table 3.11 gives a summary of the lda2
node.
Table 3.11:
Summary of the lda2 node.
Name | lda2 |
Category | Contrib/Classification |
Description | Node performs linear discriminant analysis. |
Usage | Add a matrix with values for the calibration and a vector containing the classes for the samples given in
the matrix. |
Parameters | Command |
Input ports | Input matrix, vector containing the different classes. |
Output ports | R object with the estimated classification rule. The percentwise calibration error and prediction
error. |
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The node performs a linear discriminant analysis using the scores from a principal component analysis. The
optimal number of components is found using crossvalidation. Table 3.12
gives a summary of the pcalda node.
Table 3.12:
Summary of the pcalda node.
Name | Pcalda |
Category | Contrib/Classification |
Description | Node performs lda on pca data. |
Usage | Add a matrix containing values for the calibration and a vector containing different classes. |
Parameters | Command |
Input ports | Input matrix, input vector. |
Output ports | R object with estimated classification rule, percentwise calibration error and prediction error,
loadings from the pca. |
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The node performs prediction of classes using principal analysis as preprocessing to linear or quadratic
discrimination analysis. Table 3.13 gives a summary of the pcapred node.
Table 3.13:
Summary of the Pcapred node.
Name | Pcapred |
Category | Contrib/Classification |
Description | Node performs prediction of classes based on pca before linear or quadratic discrimination analysis. |
Usage | An Pcapred node makes use of a rule from either the pcalda or pcaqda node, the loadings from either pcalda
orpcaqda and matrix with the independent variables. |
Parameters | Command |
Input ports | Classification rule, pcalda or pcaqda loadings, matrix. |
Output ports | Predicted classes. |
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The node performs quadratic discriminant analysis using the scores from a principal component analysis. The optimal
number of components is found using crossvalidation.. Table 3.14 gives a summary of the pcaqda node.
Table 3.14:
Summary of the Pcaqda node.
Name | pcaqda |
Category | Contrib/Classification |
Description | Node performs quadratic discriminant analysis using scores from a pca. |
Usage | The pcaqda operates on a matrix with indepentdent variables for the calibration, with a vector containing
the classes for the samples given in the matrix. |
Parameters | Command |
Input ports | Input matrix, and vector containign the classes. |
Output ports | R object, precentwise clibration error, prediction error and loadings from the pca. |
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The node performs prediction of classes using linear or quadratic discrimination analysis.
Table 3.15 gives a summary of the pred2 node.
Table 3.15:
Summary of the Pred2 node.
Name | Pred2 |
Category | Contrib/Classification |
Description | Node performs prediction of classes using linear or quadratic discrimination analysis. |
Usage | Add classification rule from either lda2 or qda2 node, and a matrix with independent variables as the sample
with unknown classes. |
Parameters | Command |
Input ports | lda2 or qda2 rule, input matrix. |
Output ports | The predicted classes for the unknown samples. |
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The node performs quadratic discriminant analysis. Table 3.16 gives a summary of the qda2 node.
Table 3.16:
Summary of the qda2 node.
Name | qda2 |
Category | Contrib/Classification |
Description | Node performs quadratic discriminant analysis. |
Usage | Add a matrix with independent variables for classification, a vector containing classs for the sample and a
test set. |
Parameters | Command |
Input ports | Input matrix, vector with classes, test set. |
Output ports | R object with est. class. rule, percentwise calibration error, prediction error and list of
predicted classes from the test data. |
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- AddCenter
- Anova
- CCD
- CompEffects
- FacDesign
- FracDesign
- MlrAnova
- mlr
- fssir
- MSC
- emsc
- Normalize
- OSC
- SIS
- LSPsmooth
- HCA
- Regression predict
- SciCraftPCA
- SciCraftPLS
- oldpca
- workPLS
- AddNoise
- FFT1Drows
- KNearestNeighbour
- LinearDiscrimPrediction
- LinearDiscriminantAnalysis
- PLS
- interpretpls
- predictPLS
- HierarchicalClusterAalysis
- KMeansClustering
- PCA
- AutoScale
- Correlation
- AgilentFilterRG
- AgilentLoad
- ArrayImage
- DiffExp
- FilterMA
- FilterRG
- NormBetweenArrays
- NormWithinArray
- SpikeCheck
- affytools
- bgcorrect
- genelist
- gprload
The edit node is capable of editing and transforming data in
SciCraft. Table 3.18 gives a summary of the EditNode. A
detailed description of this node is provided in section 3.3.
Table 3.17:
Summary of the dissection.
Name | Dissection |
Category | Tools |
Description | Node that can remove parts of a dataset. |
Usage | Can alter the data you use for calculations. |
Parameters | None |
Input ports | Matrix |
Output ports | Matrix |
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The edit node is capable of editing and transforming data in
SciCraft. Table 3.18 gives a summary of the EditNode. A
detailed description of this node is provided in section 3.3.
Table 3.18:
Summary of the EditNode.
Name | EditNode |
Category | Edit |
Description | Node that can remove one or several rows from a dataset. |
Usage | An edit node makes use of a command string to edit the data it
receives. Its intention in later editions of SciCraft is to make it possible to
select data in a plot node and then tell the edit node to remove these elements. |
Parameters | Command |
Input ports | commandInput - the enter point for data. |
Output ports | An exit port for the edited data. |
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This node is yet highly experimental. Use it at your own risk, and do not
expect it to behave as intended. It has basic functionality, but lacks
stability and extended functionality.
The Gaussdal node takes as input molecule data from a GaussDal database query,
and maps the molecules relative to a reference molecule. The node is connected
to Octave's Procrustes routine, running this routine on the mapped molecules.
A summary of the node is found in table 3.19. A more detailed
description can be found in section 3.4.
Table 3.19:
Summary of the Gaussdal node.
Name | Gaussdal node |
Category | Edit |
Description | Molecule mapper for Gaussdal database data. |
Parameters | Mapping parameters |
Input ports | Data from Input-node reading Gaussdal files,
column names, optional molecule mapping matrix. |
Output ports | Molecule data, mapping (not implemented yet) |
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The MoleculeEditor node is capable of showing and editing mulecules in a 3D window.
Table 3.20 gives a summary of the MoleculeEditor node.
Table 3.20:
Summary of the MoleculeEditor.
Name | MoleculeEditor |
Category | Tools |
Description | Node that can show and edit molecules in 3D. |
Usage | Node that can show and edit molecules in 3D. |
Parameters | None |
Input ports | Molecule data. |
Output ports | Molecule data. |
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Nodes capable of inspecting data currently in the nodes after running the diagrams. These nodes are summed
up in (table 3.21 and 3.22).
Table 3.21:
Summary of the ScreenDump node.
Name | ScreenDump |
Category | View |
Description | Node that is used to make plot based on calculated data in the
Module Diagram. |
Usage | This node's task is to save screendumps to file. |
Parameters | None |
Input ports | None |
Output ports | Imagefile |
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The spreadsheet node may take several matrices, vectors and scalars on
its input port and display them in a spreadsheet.
Table 3.22 gives a summary of the SpreadSheet
Node, while a more detailed description is presented in
section 3.5.
Table 3.22:
Summary of the SpreadSheet Node.
Name | SpreadSheet Node |
Category | View |
Description | Node that displays the selected data in a familiar spreadsheet. |
Usage | View matrices, vectors and scalars in a spreadsheet representation. It is possible to save all the data
that is in the spreadsheet to file, and to make selections which may be copied to the clipboard, for pasting it into
another application. |
Parameters | None |
Input ports | matrices - the entry point for data. |
Output ports | None |
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SciCraft Development Team