Systrip developer manual
Contents
1. 0 81 Public members 3 0 8 2 PluginProgress 3 0 9 Example of a plug in skeleton 2 252 RUE x em Re EE 3 0 10 Metabolic network specific properties Systrip developer manual List of Tables 2 1 Requirements table 2 2 Tulip required plug ins 2 3 Common CMake options for Systrip Systrip developer manual 1 14 Chapter 1 Introduction With the development of high throughput methods in biology efficient visualization tools are more and more required In particular it helps in understanding biological shifts induced on an organism by environmental stresses In that case the data generated covers a wide range of biological processes which can be gathered into a single network This network generally contains hundreds of elements and prior to any in depth analysis biologists are used to reduce the scope of their studies by selecting a few relevant sub networks The visual analytic process thus follows a top down approach consisting in filtering out steady part of the network To help users in this visual mining we propose a flexible environment called Systrip Systrip is a perspective dedicated to biological network analysis and takes full advantage of the Tulip library and plug in sys tem More than simply using Tulip library Systrip adds a network manipulation layer on top of it S2. he pressed stop all values computed till now will be saved to the graph 3 0 9 Example of a plug in skeleton Following is an example of a dummy color algorithm you can find more example in the tulip tarball include lt tulip TulipPlugin h gt include lt string gt using namespace std using namespace tlp Algorithm documentation MyColorAlgorithm is just an example x Systrip developer manual 11 14 class MyColorAlgorithm public ColorAlgorithm SULS L The constructor below has to be defined it is the right place to declare the parameters needed by the algorithm addParameter DoubleProperty metric paramHelp 0 0 false and declare the algorithm dependencies too addDependency Algorithm Quotient Clustering 1 0 MyColorAlgorithm const PropertyContext amp context ColorAlgorithm context Define the destructor only if needed MyColorAlgorithm 1 gr Define the check method only if needed It can be used to check topological properties of the graph metric properties on graph elements or anything else you need bool check string amp errorMsg errorMsg 72 return true 207 The run method is the main method Jd It will be called out if the pre condition method bool check returned lt gt true It is the starting point of your algorithm The returned value must be true if your algorithm succeeded bo
3. integer indicating the charge on the species in terms of electrons not the SI unit coulombs constant BooleanProperty Indicates whether the species quantity can be changed at all regardless of whether by reactions rules or constructs other than InitialAssignment compartment StringProperty Only for compounds nodes The compartment represents a bounded space in which species are located ecNumber StringProperty Only for reaction nodes Correspond to the Enzyme Commission number EC number for the reaction The EC number is a numerical classification scheme for enzymes based on the chemical reactions they catalyze elmentType IntegerProperty Indicates the node type If the value is O the element type is undefined 1 is for species and 2 for reactions fastReaction BooleanProperty See the fast attribute in the SBML specification geneAssociation StringProperty hasOnlySubstanceUnits BooleanProperty See the hasOnlySubstanceUnits attribute in the SBML specification id StringProperty The id of the elements from SBML file Each nodes have unique id initialAmount DoubleProperty Values are defined only for compounds nodes It represents species initial quantity initialConcentration DoubleProperty See initialConcentration attribute in SBML specification listOfProducts Integer VectorProperty Only for reaction nodes For ea
4. Systrip developer manual Systrip developer manual Systrip developer manual COLLABORATORS TITLE Systrip developer manual ACTION NAME DATE SIGNATURE WRITTEN BY May 30 2011 REVISION HISTORY NUMBER DATE DESCRIPTION NAME Systrip developer manual Contents 1 Introduction 2 Installation 2 1 Requirements e koe We Rex eA Rc om ee a uh E ee S SR Y E me 2 2 Compilation oo Roh on f Roh a how eA e Ro E 224 Systup compilation ioo s GS Re GA o RU A VON EUR FU S RO Em HRE s 3 2 2 2 LibSBML compilation 2 42 4 4 2 2 3 OpenBabel compilation 22 4 FEMPEG compilation sons e sa DEE ox em ER P ROCK S ER Est E 3 2 223 GSOAP compilation 22 52 2225 e ORO URL Rh 3 Plug ins development 3 0 6 Overviewol the class ys ie BA ea dede quemque BAY Eee s 3 0 6 1 Public members 3 0 6 2 Protected members 2 07 Parameters vs a ee hae UE a de ee Ue Rel Ge deh we A 3 0 7 1 Adding parameters to an algorithm LL 3 0 7 2 Accessing a parameter 4 lel LL 3 0 8 The Plusinbrosress Class aren er Ba rn eee pa EE ede 3
5. ch reaction node this property contain the list of it s products Each integer in the list correspond to a node id listOfReactants Integer VectorProperty Only for reaction nodes For each reaction node this property contain the list of it s reactants Each integer in the list correspond to a node id name StringProperty The name of the elements proteinAssociation StringProperty reaction BooleanProperty For each nodes Defines the type of the element if set to true the node is a reaction else it s a compounds Systrip developer manual 13 14 Property name Property type Description Only set for reaction nodes If a reversible BooleanProperty reaction has this value to true so this reaction is reversible The list of pathways names in which subSystem String VectorProperty each node compound or reaction is present Only for edge This property contains the stoichiometry attribute of the stoichiometry DoubleProperty SBML file It s the factor applied to the reaction rate to give the rate of change of the species Here is a short color algorithm sample to color reaction nodes in blue and species nodes in red include lt tulip ForEach h gt include lt tulip ColorAlgorithm h gt using namespace tlp using namespace std Algorithm documentation SpeciesAndReactionColorAlgorihtm will color reaction nodes in blue and species nodes
6. clean 7 You can now launch Tulip and enjoy Systrip by launching the tulip program in the bin subdirectory of the installation directory See user manual for more information on Systrip usage There is an issue when linking with the dynamic version of OpenBabel when closing Systrip an error can occur during the destruction of OpenBabel plug ins This error don t affect the program usability To fix it link with the static version of OpenBabel see OpenBabel compilation for more information 2 2 2 LibSBML compilation LibSBML uses the autotools to configure it s build You don t need to set special build options to use it with Systrip THE SIMPLEST WAY TO COMPILE IT IS 1 Go into the source directory of LIBSBML 2 Configure the build process with the configure script configure Check the build configuration log to see if there is some errors 3 Type make to compile the package 4 make install to install it 5 You can remove the program binaries and object files from the source code directory by typing make clean If you need more help with LibSBML compilation see the it s website http sbml org Software libSBML 2 2 3 OpenBabel compilation OpenBabel uses Cmake as build system To avoid the error when closing Systrip just set the BUILD SHARED variable to OFF If you re compiling on 64 bit system you will need to add fP IC to CMAKE CXX FLAGS THE SIMPLEST WAY TO COMPILE THIS PACKAGE IS 1 Create a dir
7. documentation Documentation can be found in the buildDirectory controller docs subdirectories TULIP_DIR Path Tulip installation directory OPENBABEL2_DIR Path OpenBabel installation directory GSOAP_PATH Path Gsoap installation directory LIBSBML_INCLUDE Path Libsbml includes directory LIBSBML_LIBRARY File Libsbml library FFMPEG_DIR Path FFMPEG installation directory MYSQL_DIR Path MYSQL installation directory None Debug CMAKE BUILD TYPE Release Rel WithDebInfo MinSizeRel COMPILE_TESTS boolean Control the build type Table 2 3 Common CMake options for Systrip THE SIMPLEST WAY TO COMPILE THIS PACKAGE IS 1 Create a directory where the package will be build 2 Configure the build process with cmake buildDirectory sourceDirectory cmakeOptions Check the build configuration log to see if there is some errors 3 Go to the build directory if you re not in 4 Type make to compile the package Systrip developer manual 4 14 5 Typemake install to install Systrip inside the Tulip directory On windows system files can be installed in the wrong directory and you had to move them manually To check it go into the Tulip installation directory in the lib directory check if there is a bin directory if it exists copy all its files into the t 1p directory 6 You can remove the program binaries and object files from the source code directory by typing make
8. e which is capable of adding a parameter This method has to be called in the constructor of your class Following is a description of its parameters name Name of the new parameter inHelp This parameter can be used to add a documentation to the parameter See example below inDefValue Default value isMandatory If false the user must give a value On the following example we declare a character buffer that will contain the documentation of our parameters Systrip developer manual 8 14 namespace const char paramHelp property HELP OPEN HELP DEF type DoubleProperty HELP BODY N his metric is used to affect scalar values to graph items he meaning of theses values depends of the choosen color model HELP CLOSE colormodel ELP OPEN ie Veel Viar c SUE Dur Wd y X HES ime Si ane 0 Wool 4 S ELP_BODY his value defines the type of color interpolation Following values are valid 1 gt lt 11 gt 0 HSV interpolation lt 11 gt lt 11 gt 1 RGB interpolation lt li gt lt ul gt X HELP CLOSE Colom HELP OPEN BIEL Ie RD CUIR ONE LN MN values VO sms Das Tofauti Wied X HELP BODY I This is the star
9. ectory where the package will be build 2 Configure the build process with cmake cmake buildDirectory sourceDirectory cmakeOptions DBUILD SHARED OFF Check the build configuration log to see if there is some errors 3 Go to the build directory if you re not in 4 Type make to compile the package 5 Type make install to install OpenBabel 6 You can remove the program binaries and object files from the source code directory by typing make clean Checks the OpenBabel site if you need more help for building it http openbabel org wiki Main Page Systrip developer manual 5 14 2 2 4 FFMPEG compilation FFMPEG uses the autotools to configure it s build There is some special options to set to use FFMPEG with Systrip enable gpl enable memalign hack enable swscale THE SIMPLEST WAY TO COMPILE IT IS 1 Go into the source directory of FFMPEG 2 Configure the build process with the configure script configur nable gpl nable memalign hack nable swscale Check the build configuration log to see if there is some errors 3 Type make to compile the package 4 Typemake install to install it 5 You can remove the program binaries and object files from the source code directory by typing make clean If you need more help with FFMPEG compilation see the it s website http ffmpeg org 2 2 5 GSOAP compilation You don t need to compile GSOAP to use it with Systrip Just set the GSOAP_PATH to the sou
10. er into the corresponding property of the graph Following is a table showing the data member graph property and Algorithms GUI sub menu corresponding to each subclass of Algorithm Class name Data member Graph property replaced BooleanAlgorithm booleanResult viewSelection ColorAlgorithm colorResult viewColor DoubleAlgorithm doubleResult viewMetric Integer Algorithm integerResult viewInt LayoutAlgorithm layoutResult viewLayout SizeAlgorithm sizeResult viewSize StringAlgorithm stringResult viewLabel 3 0 6 Overview of the class A quick overview of the functions and data members of the class PropertyAlgorithm is needed in order to have a generic under standing of its 8 derived classes 3 0 6 1 Public members Following is a list of all public members PropertyAlgorithm const PropertyContext amp context The constructor is the right place to declare the parameters needed by the algorithm addParameter DoubleProperty metric paramHelp 0 0 false And to declare the algorithm dependencies addDependency Algorithm Quotient Clustering 1 0 Systrip developer manual 7 14 e PropertyAlgorithm Destructor of the class bool run This is the main method It will be called out if the pre condition method bool check returned true It is the starting point of your algorithm The returned value must be true if your algorithm succeeded bo
11. in red This is just an example to show how to use algorithm with Systrip properties 8 class SpeciesAndReactionColorAlgorihtm public ColorAlgorithm Pabo SpeciesAndReactionColorAlgorihtm const PropertyContext amp context ColorAlgorithm context lt gt SpeciesAndReactionColorAlgorihtm bool check string amp errorMsg Check if isReaction property exist if graph existProperty reaction return false selse errorMsg Reaction property don t exist this graph is not a Systrip graph LIBUS ioco a Get the reaction property BooleanProperty isReaction graph gt getProperty lt BooleanProperty gt reaction For each nodes test if the node is a reaction or a species node n forEach n graph gt getNodes The node is a reaction if isReaction gt getNodeValue n colorResult setNodeValue Color 0 0 255 jelse The node is a species colorResult setNodeValue n Color 255 0 0 Systrip developer manual 14 14 return true x Register plug in COLORPLUGIN SpeciesAndReactionColorAlgorihtm Species and reaction color Authors lt gt Wr Eemere AE OW
12. ments a container which allows insertion of values of different types and implements the following methods template typename T bool get const std string amp name T value const Returns a copy of the value of the variable with name name If the variable name doesn t exist return false else true template typename T bool getAndFree const std string amp name T value Returns a copy of the value of the variable with name name If the variable name doesn t exist return false else true The data is removed after the call template typename T void set const std string amp name const T value Set the value of the variable name bool exist const std string amp name const Returns true if name exists else false Iterator lt std pair lt std string DataType gt gt getValues const Returns an iterator on all values Has you could have guess the one important to access a parameter is get which allows to access to a specific parameter Following is an example of its use DoubleProperty metrics int colorModel Calon bool mappingType true if dataSet 0 dataSet gt get property metrics dataSet gt get colormodel colorModel dataSet get colorl colorl dataSet get color2 color2 dataSet gt get type mappingType 3 0 8 The PluginProgress class The class PluginProgress can be used to interact with the user Follo
13. name Plug ins type Required version Document View View 1 0 Histogram view View 1 0 Parallel Coordinates view View 1 0 Table view View 1 0 Scatter Plot 2D view View 1 0 FM 3 OGDF Layout 1 0 Table 2 2 Tulip required plug ins Systrip developer manual 3 14 To use Systrip plug ins you had to have certain plug ins not installed by default To get these plugins use the Tulip plug ins manager see the Tulip user manual chapter 4 section 3 for more information 2 2 Compilation 2 2 1 Systrip compilation The Systrip build process uses CMake to guess correct values for various system dependent variables used during compilation It uses those values to create a Makefile for each directory of the package It may also create or more h files containing system dependent definitions To get CMake or for more information see the CMake website You can add some option to the default build process with CMake Option Type Comments compile unitary tests To run unitary tests just launch the buildDirectory controlle r MetabolicNetworkExplor erController Tests Test program You need to have Systrip installed in Tulip before launching the tests You may have to configure the TLP_DIR environnment variable to tell where the Tulip plugins are located see Tulip documentation for more information on this variable Compile documentation Documentation consist in a user manual a developer manual and api COMPILE_DOC boolean
14. ol 1 return true x This line is very important because it s the only way to register your algorithm in lt eben It automatically builds the plug in object that will embed the algorithm COLORPLUGIN MyColorAlgorithm My Color Algorithm Authors 07 07 07 Comments lt OS If you mant to present your algorithm in a dedicated sub menu of the Tulip GUI use the declaration below where the last parameter specified the name of sub menu COLORPLUGINOFGROUP MyColorAlgorithm My Color Algorithm Authors 07 07 07 lt Comments 1 0 My algorithms 3 0 10 Metabolic network specific properties If you develop plug ins for Systrip you can access to certain properties loaded from the SBML file these properties contains useful information on the network The next table describes the list of these properties with their types and description Systrip developer manual 12 14 Property name Property type Description boundaryCondition BooleanProperty Only for compounds nodes Can have true or false values Define if the compounds is a boundary species i e if it s quantity is not determined by the set of reactions even when that species occurs as a product or reactant If true the species is on the boundary of the reaction system and its quantity is not determined by the reactions charge IntegerProperty The charge property takes an
15. ol check std string amp errMsg This method can be used to check what you need about topological properties of the graph metric properties on graph elements or anything else 3 0 6 2 Protected members Following is a list of all protected members e Graph graph This graph is the one given in parameters the one on which the algorithm will be applied e PluginProgressx pluginProgress This instance of the class PluginProgress can be used to have an interaction betvveen the user and our algorithm See the next section for more details e DataSetx dataSet This member contains all the parameters needed to run the algorithm The class DataSet is a container which allows insertion of values of different types The inserted data must have a copy constructor well done See the section called DataSet for more details The methods of the TypeNameAlgorithm class will be redefined in your plug in as shown in Section 3 0 9 3 0 7 Parameters Your algorithm may need some parameters for example a boolean or a property name that must be filled in by the user just before being launched In this section we will look at the methods and techniques to do so 3 0 7 1 Adding parameters to an algorithm The class PropertyAlgorithm inherits from a class called WithParameters that has a member function named template lt typ name Type void addParameter const char name const char 1 0 const char inD efValue 0 bool isMandatory tru
16. rce path of GSOAP Systrip developer manual 6 14 Chapter 3 Plug ins development Systrip is based on Tulip plug ins system It enables to directly add new functionalities into the Systrip kernel One must keeps in mind that a plug in have access to all the parts of Tulip Thus one must write plug ins very carefully to prevent memory leak and also errors A bug in plug in can result in a core dump in the software that uses it To enable the use of plug ins a program must call the initialization functions of the plug ins This function loads dynamically all the plug ins and register them into a factory that will enable to directly access to it The PropertyAlgorithm class is the class from which inherits different types of algorithms such as the BooleanAlgorithm class or the LayoutAlgorithm class see picture below This class is important in the way that every specific algorithm that you will develop will have to inherit from one of those classes For example if you write a plug in to update the graph layout your new class will have to inherit from the LayoutAlgorithm class which inherits from this PropertyAlgorithm class doxygen tulip lib classtIp_l_1PropertyAlgorithm__inherit__graph png not found Each one of the 8 classes presented above has a public mem ber TypeNameProperty typeNameResult which is the data member that which have to be updated by your plug in After a successful run tulip will automatically copy this data memb
17. t color used in the interpolation process N H ESE SEO SIBI Uer HELP OPEN d Duo Evet VOogdiou y X H RS Dan E ZAL eN H rasent N H HELP BODY X This is the end color used in the interpolation process H HBP CHOSE P Mapping type H HELP OPEN H _ HELP DEF type Boolean H CE Ibis Ar M S N H RIMES Dan octau eN H HELP BODY This value defines the type of mapping Following values are valid lt ul gt lt li gt true linear mapping lt li gt lt li gt false uniform quantification lt li gt lt ul gt I I E A Ha OR gg E ord kd d kl Jl HA A JA A BEA A HA EAE H H Ek HELP CLOSE Then we can add the parameters in the constructor by writing the following lines addParameter DoubleProperty property paramHelp 0 viewMetric addParameter lt int gt colormodel paramHelp 1 1 addParameter bool type paramHelp 4 true addParameter lt Color gt colori paramHelp 2 255 255 0 128 addParameter lt Color gt color2 paramHelp 3 0 0 255 228 The picture below is the result of the sample of code above images plugin_doc_add_parameter_1 png not found Systrip developer manual 9 14 3 0 7 2 Accessing a parameter The class Property Algorithm has a protected member called dataSet that contains all the parameters value The DataSet class imple
18. uch architecture aims at encapsulating both of graph manipulation and user interaction libraries Relying on a graph structure gives to Systrip a great flex ibility allowing to support both relational and multi dimensional data It also simplifies future integration of different biological networks e g gene regulatory network or protein protein interaction network This document describes technical information for Systrip as it is based on the Tulip library you can find more detailed informa tion on Tulip documentation See Tulip documentation web page Systrip developer manual 2 14 Chapter 2 Installation 2 1 Requirements To work properly Systrip need some dependancies referenced in the next table Library Required version CMake gt 2 6 Tulip 3 4 1 Qt gt 4 6 x or Qt 4 7 with QtAssistantClient not installed by default in Qt 4 7 OpenBabel gt 2 2 3 FFMPEG 0 5 GSoap gt 2 7 libSBML gt 4 3 MYSQL LibXML2 zlib freetype glew libjpeg libpng DoxyGen for documentation only dblatex for documentation only Table 2 1 Requirements table Systrip is not a program itself it s just an add on for Tulip system so installing Systrip on your system consists in fact to copy files into your Tulip installation directory After installing Systrip run Tulip and you can use Systrip from the Tulip interface Plug ins
19. wing is a list of its members 3 0 8 1 Public members Following is a list of all Public members ProgressState progress int step int max step This method can be used to know the global progress of or algorithm the number of steps accomplished void showPreview bool Enables to specify if the preview check box has to be visible or not bool isPreviewMode Enables to know if the user has checked the preview box Systrip developer manual 10 14 ProgressState state const Indicates the state of the Cancel Stop buttons of the dialog void setError std string error Shows an error message to the user void setComment std string msg Shows a comment message to the user 3 0 8 2 PluginProgress example In following small example we will iterate over all nodes and notify the user of the progression unsigned int i 0 unsigned int nbNodes graph numberOfNodes const unsigned int STEP 10 node n forEach n graph getInEdges n Do what you want if i STEP 0 pluginProgress gt progress nbNodes Says to the user that the algorithm has progressed exit if the user has pressed on Cancel or Stop if pluginProgress state CONTINUE returnForEach pluginProgress state TLP CANCEL Lg Before exiting we check if the user pressed stop or cancel If he pressed cancel the graph will not be modified If
Download Pdf Manuals
Related Search