Systrip User Manual - Tulip
Contents
1. RORSE e GE E eh RU 23 2 4 1 Visual parameters non ao a 23 24 2 Information lables ss i25 eevee be So be eked eo A eae OR BES 9 9 ede Se oU BH 24 2 4 3 Metabolic plug ins list 24 Features 25 3 1 Network or metabolic views visualization fs 3 2 Dataset visualiZation creation was See he kauae udk e o9 Re m obe RE E 26 aur 100 21 3 4 Register video from view PA 3 5 Query more information in distant 28 AMEN e E GENEE ENEE eee ee EEN 28 35 ETH 29 3 6 Adding new algorithms s 0 29 Systrip User Manual V List of Figures Lll SYSWip udi VIEW s sp 24542 Ge AO Seed 9 9 ox x Rees OR oe OR E ok rd RC Sos d 1 2 1 Decomposition of the Systrip graphical user 1 2 22 bat and neni toolbar ec ow oos m oe x Are eh e s OX m EG SG Ee 3 2 4 24 5 2 5 Metabolic network widget interface description 2 a e 6 2 6 Add an element by drag and drop 7 2 7 Creation of metabolic view by dragging a pathway on view workspace 8 2 8 Creation of metabolic view by dragging a pathway on2. ko01064 Biosynthesis of alkaloids derived from ornithine lysine and nicotinic acid PATH ko01065 Biosynthesis of alkaloids derived from histidine and urine PATH ko01066 Biosynthesis of alkaloids derived from terpenoid and kend olyketide PATH ko01070 Biosynthesis of plant hormones PATH ko01100 Metabolic pathways PATH ko02020 Two component system 2 3 3 1 2 3 3 3 2 3 3 8 2 8 3 10 3 4 13 20 4 1 3 6 4 2 13 4 2 1 4 2 3 2 27 KNApSAcK C00007619 PDB CCD CIT 3DMET B00046 NIKKAJI J2 824J KCF data Show 1 o Go Back All links Ontology 1 KEGG BRITE 1 Pathway 4631 KEGG PATHWAY 4627 KEGG MODULE 4 Drug 10 KEGG DRUG 10 Chemical substance 27 PubChem 1 Chemical reaction 27 KEGG ENZYME 10 KEGG REACTION 8 KEGG RPAIR 9 All databases 4696 Figure 2 22 Information view two state preview and detailed mode The preview mode prints a screenshot of all the selected data and when user double clicks on a screenshot the view switches to detailed In the detailed mode the user can interact with a real HTML page This page contains all the information found on the element in the databases User can click on an hyperlink that will create a new screenshot on the preview mode 2 3 2 1 View operations In the preview mode user can move or zoom on preview If user waits with the mouse pointer on a preview a tool tip appears with the node number and the URL of t
3. spermine bi putrescine 7 29 b Unclassified elements Figure 2 6 Add an element by drag and drop To delete elements user can either use the contextual menu or press the Del or Backspace key Removing an element in a pathway subtree removes it from the pathway When an element no longer belongs to any pathway it will be displayed in the Unclassified elements inner node Deleting an element from the Unclassified elements inner node removes it definitely 2 2 1 1 1 Contextual menu By right clicking on this widget user can show a contextual menu This menu differs in function of the selected element type Rename only visible when clicking on pathway item Rename the selected pathway e Show properties display the available information on the selected element pathway compounds or reaction Select Deselect select all unselected or partially selected elements and unselect others Delete delete the selected element If it s a pathway these internal elements will not be erased Create new pathway create an empty pathway e Create new pathway from selection create a new pathway with current selection as base elements 2 2 1 2 Metabolic views widget This widget allow user to create delete and edit metabolic views This widget is similar to the network widget presented before Each metabolic view is represented in the tree widget by inner nodes regrouping
4. Network Navigation Figure 2 7 Creation of metabolic view by dragging a pathway on view workspace You can also drop the selected element on the view workspace this solution create a new view and draw them immediately Systrip User Manual 9 29 File Edit Metabolic Network Information Windows Help bei Eet E Maat Info Editor amp home jdubois workspace Tulip 3 3 1 testHetaMap Leishmania major e Nodes 1040 Edges 1062 Id v Name gt UDP N acetyl D galactosamine biosynthesis Il UDP N acet gt UDP N acetyl D glucosamine biosynthesis II UDP N acet UDP glucose conversion UDP glucos UTP glucos UDP galactose UDP D gluc UDP glucos UTP gt Unclassified elements aerobic respiration electron donors reactio aerobic resp dihydroxy a fumarate DI ee gt Views Id Nam New view New UDP glucos Display pathways Display compounds V Display reactions e Al Elements Selected Elements Network Navigation Element properties Figure 2 8 Creation of metabolic view by dragging a pathway on metabolic view widget For the both methods when creating a new metabolic view a dialog appears to query its name If you enter an existing name an error message will appear and the creation will be canceled Choose the name for the new view Figure 2 9 Metabolic view
5. Pathway 8 6 P NAD bios NAD biosynt Pathway P nitrate re nitrate redu Pathway N acetylglucosamine 1 phosphodiest r alp ac yrgnucosamine s pnospn i EN P glutamin glutamine bi Pathway droflavonol NA acetol asemiquinone N acetyl D gl cos b 4 amino 4 aminobut Pathway b phosphol phospholipa Pathway P degradat degradation Pathway P salvage salvage pat Pathway gt GDP L fu GDP L fucos Pathway P isoleucin isoleucine d Pathway t emialdehyde oxalosuccinate 4 amp amp alpha carboxy 4 amp amp beta me 2 hydr xygl b glutathio glutathionyl Pathway f gt 4 amino 4 aminobut Pathway um Ota Aconitate hydratase L arginin D is citrate Blpha ketoglutarate Views Citrate si synthase malate e Name cis aconitate N N i New view PM Aconitate hydratase v TCA cycle ethylubiquinone 8 5 methylthioribdgse Citrate4Si synthase oxal acetate Aldehyde red D inositgH 1 4 Disphosphate 1203 alditol 44 4 5 trisphosphate aldehyde naw indole 3 glyo N nitrile a indole 3 glyg indole 3 4 Aconit SER Ni ester dGDPT 4 Display pathways V Display compounds V Display reactions atty aldehyde amp All Elements Selected Elements Network Navigation Element properties Data Sets Figure 2 10 Metabolic view selection example 2 2 1 2 1 Contextual menu
6. elements are unselected or partially selected select them else unselect them Augmented display only visible when a data set is selected the augmented display selection menu is used to apply or remove specific information over each element of a data set See the augmented display section Section 2 4 for more information on elements you can display over data sets nodes Import new data set import a new data set If you want more details on data sets importation see Section 2 2 3 1 3 Delete delete the selected element data set or node If the element is a node remove it from the data set Delete all data sets remove all the data sets 2 2 3 1 2 Augmented display This widget allows user to display augmented information for the selected data set Select the information you want to display and click on the apply button To hide displayed information choose the No display value and click on apply Here is a list of the kind of information you can display over data set elements e Display heat maps display the heat map information Each time point is represented by a rectangle The rectangle s colour depends on the value of the represented time point The colours are computed this way we divide the data set values interval in ten parts and we map a colour for each parts Systrip User Manual 15 29 L aspartate Figure 2 15 Heat map Figure 2 16 Heat map colour mapping Curve build a curve with values of the node
7. for elements in the reactions Pathways search for elements in the pathways Preferences displays the preferences dialog Advanced mode check button to switch from simple to advanced user interface e Metabolic network contains all the actions related to the metabolic network Import network loads a metabolic network in Systrip from an sbml file Only one network can be loaded after the button is disabled Redraw current view Ctrl R erase the old layout perform a new one for the selected widget Redraw network redraw the root network layout If network widget does not exist create new one Restore default parameters restore the visual parameters defined in the preferences dialog for the metabolic network and all its views Analysis from this menu you can apply analysis algorithms on the selected view The algorithms present in this menu are specially designed and configured to work with metabolic networks They are separated in distinct types x Graph measure this sub menu is populated by metric algorithms These algorithms allow to compute and assigne a value to the viewMetric property of graph elements For example when running the Degree algorithm the degree the number of a node neighbors of each node is computed and stored in the viewMetric property Biological selection this sub menu is populated by selection algorithms These algorithms allow to select nodes and or edges sati
8. it is selected you can edit the bends of an edge by first selecting the edge using the mouse left button Then a mouse left click with the Shift key pressed will add a new bend moving the mouse with the left button pressed will allow to move an existing one a mouse left click on a bend with the Ctrl key pressed Alt key on Mac will remove it 2 k Get Information when this operation is selected if you click on an element of a graph node or edge displays all available information of that node edge using the Elements properties widget tab of the Dock widget sub window see Section 2 2 2 1 lt p Highlight neighborhood this interactor allows to get information regarding the neighborhood of a node by highlighting the nodes connected to it A Bring and Go feature is also implemented allowing to navigate from close to close in a graph with smooth animations First click on a node to select it next you can either click again on it and select a neighbor to navigate to it or use the mouse wheel to modify the neighborhood selection distance Magnifying glass this interactor provides a magnifying glass tool for all Tulip views It allows to zoom on a particular area of a visualization with the help of a lens without having to modify the global zoom level Move the mouse on the screen to move the lens Use Ct r1 the mouse wheel to enlarge or reduce the lens radius Use shift the mouse wheel to improve or reduce the zoom level 2 3 1
9. its pathways reactions and compounds nodes There are two ways to create a new metabolic view The first by using contextual menu on the metabolic view management widget Select the Create new vieworCreate new view from selection menu see Section 2 2 1 2 1 The second solution is to drag and drop elements from metabolic network widget There is multiple drag and drop possibilities from the network widget First you can simply drag pathway or element from the network widget to the metabolic view widget be sure to don t drop element on an existing view or you will modify it This solution simply creates a new view with the dragged element as base element Systrip User Manual 8 29 File Edit Metabolic Network Information Windows Help a NM at Info Editor x home jdubois workspace Tulip 3 3 l testHetaMap Up Leishmania major e Nodes 1040 Edges 1062 Id v Name gt UDP N acetyl D galactosamine biosynthesis II UDP N acet gt UDP N acetyl D glucosamine biosynthesis II UDP N acet UDP glucose conversion UDP glucos UTP glucos UDP galactose UDP D gluc UDP glucos UTP gt Unclassified elements aerobic respiration electron donors reactio aerobic resp dihydroxy a fumarate UDP glucose cfaversion UDP glucos 7 New view v UDP N acetyl D glucosamine biosynthesis II Display pathways W Display compounds M Display reactions e Al Elements Selected Elements
10. state Save Ctrl S save the current state in a Tulip graph If there is an older one save overwrites with new data m Print Ctr P a Search in all elements Ctrl F search for elements in the full graph Ze Systrip User Manual 5 29 Import network load a metabolic network in Systrip from an sbml file Only one network can be loaded when it s done the button is disabled e Redraw current view Ctrl R if a metabolic network view is selected in the view workspace erase the old layout Ca perform a new one for this view Record selected view create a video from the activated view If the selected is not compatible with video recording this icon is disabled e 2 2 Dock widget This is the main widget for interact with data loaded in Systrip It contains data manipulation widgets like metabolic network widget or data sets widget Here is the list of the widget you can find in the dock widget Network navigation metabolic network navigation and manipulation e Element properties properties visualization for selected nodes Data sets data sets management widget Advanced options only visible in advanced mode Contain the view interactors and video configuration widgets To switch between the different widgets just click on the corresponding tab at the bottom of the dock widget Network Navigation Element properties DataSets Advanced options Figure 2 4 Dock widget tabs 2 2 1 Metabo
11. 2 4 Preferences dialog This widget regroup all the configuration parameter for Systrip Parameters are divided in three group represented by a tab in this dialog To apply modifications done in any tab just click on the Ok button 2 4 1 Visual parameters These parameters affect all the network drawings Reversible reactions node color the color for reversible reactions e Reversible node color the color for way reactions Compounds node color the color for all the compounds Systrip User Manual 24 29 e Interpolate edge color from nodes when checked the edge color is interpolated from the color of its source node to the color of its target node e Compound to reaction edges if the color is not interpolated this property define the color of all edges starting from a compound and ending to a reaction e Reaction to compound edges if the color is not interpolated this property define the color of all edges starting from a reaction and ending to a compound Reactions label property the property to use as reactions label Compounds label property the property to use as compounds label Nodes size the size of node for reactions and compounds e Use edge size interpolation if checked edge and edge extremities sizes are computed from node size and re spectively Edge size and Edge extremities size parameters If unchecked edge and edge extremities sizes are respectively Edge sizeandEdge extremities size parameter
12. 2 Contextual menu Save picture as take a snapshot of the view and save it in the selected format Dialog display or hide the 3D overview Hide Show label display or hide elements labels Hide Show arrows display or hide edge extremities arrows An arrow is used to show if the reaction is reversible or not If the reaction is reversible the edge will have an arrow at each of this extremities else only one edge is visible Center view center the view Systrip User Manual 2 3 1 3 Configuration widget 21 29 This widget is used to configure the background color for the view To change it click on the Background color button select the new color and click on the Apply button 2 3 2 Information view This view is used to display information from databases and to interact with There are two states for this view mode and the detailed mode the preview E COMPOUND C00158 C00158 Compound Citrate Citric acid 2 Hydroxy 1 2 3 propanetricarboxylic acid 2 Hydroxytricarballylic acid Formula C6H807 Mass 192 027 HO kO HO 2 07 OH C00158 Same as D00037 BRITE hierarchy Reaction R00351 R00352 R00362 R01322 R01323 R01324 R01325 R04357 89 Pathway PATH ko00020 Citrate cycle TCA cycle ropanoids PATH ko01062 Biosynthesis of terpenoids and steroids PATH ko01063 Biosynthesis of alkaloids derived from shikimate pathway PATH
13. By right clicking on this widget user can show a contextual menu This menu differs in function of the selected element type Rename only visible when clicking on pathway item rename the selected pathway Show properties display the available information on the selected element pathway compounds or reaction Select Deselect select all unselected or partially selected elements and unselect others Delete delete the selected element from the network If the deleted element is an internal element it will be definitely lost If the element is a pathwa y these internal elements will be not erased Create new pathway only visible when a view is selected create a new pathway with no elements Create new pathway from selection only visible when a view is selected create a new pathway with current selection as base elements Create new view create an empty new view Create new view from selection create new view with current selection as base elements 2 2 1 3 Tree widget elements control widget This widget controls the display of tree widget elements for both metabolic network and metabolic network view widgets It allows to display elements according to their types compounds reactions pathways and their states selected or not 4 Display pathways lb Display compounds Display reactions All Elements Selected Elements Figure 2 11 Elements display control buttons Systrip User Manual 11 29 The first
14. PATHWAY 4702 KEGG MODULE 4 Drug 10 KEGG DRUG 10 Chemical substance 27 PubChem 1 ChEBI 1 3DMET 1 HMDB 1 KNApSAcK 1 MASSBANK 20 NIKKAJI 1 PDB CCD 1 Chemical reaction 27 KEGG ENZYME 10 KEGG REACTION 8 KEGG RPAIR 9 All databases 4771 Figure 1 1 Systrip main view Systrip User Manual 2 29 Chapter 2 Graphic Interface This chapter describes all the Systrip perspective user interface The next picture shows the main organization of the Systrip interface Menu bar amp P ber View tools toolbar View workspace Leishman La cR i 1 x rycin thes bike C Ech 87 kr A cyrim ree au beg pk Reie 1 TAT Sch gt mrte wap emp betad D gluto se 6 phosphate Giucase e phosphate isomerase malake nla uche ap 4 pele mace zitembe alu se Ba oan acid M Dlepem ate i D giseeralgehyc 3 phesphate riboflavin Ce isomerase Dock widget D Coordnetes view Try penoSangerIpem_medfiedo 2 D v Gi Information View 7 TA Geck RD ie XP NE i ad Ga Oech b b Usckooted Klee COMPCUNUD CODT5B Cara Sik eed 24 2 3 propengi cae c 74 hirap certs bee Gi phras of compo d napilay rara alaml
15. RO P bb E RE UR EE 3 1 Metabolic representation configuration dialog 23 3 2 Data set representation creation 26 3 3 View type Selection screen s o Ow A bE ROE SOR ROROE E de ke deb SEHR ee RR RR Ee REEDED 26 34 Time points selection screen o sb HE oko R33 m Rod Ro HRS SOE EE A o 4 PO C RR ROG 33 27 3 5 Database priority edition widget 28 Systrip User Manual 1 29 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 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 net
16. Systrip User Manual Systrip User Manual Systrip User Manual COLLABORATORS TITLE Systrip User Manual ACTION NAME DATE SIGNATURE REVISION HISTORY NUMBER DATE DESCRIPTION NAME Systrip User Manual Contents 1 Introduction 2 Graphic Interface 2 1 Menu bar and menu tool bar llle ee Zu CT DAE x EENHEETEN OPE EN 2 1 2 Mena s seis oe x0 959 xx 4 ow EP ES REG 2 2 DOCK WEISS s sm 2 2 1 Metabolic network navigation widget 2 2 1 1 Metabolic network widget 222222 ss 22 1 1 1 Contextualmenu 2 2 2 2224222 ros 2 2 1 2 Metabolic views widget 22 2 ContexDlal menm ss e sae ee AE A EE e 2 2 1 3 Tree widget elements control widget 2 214 Elements properties Widget gt lt es asst RE 4 ROB Cs m XE 4X Xo c5 dede ESS 22 gt DAA SEN ava ce bee Gene Pom eee EUR amp ROPA d s 2 2 3 1 Data sets management menn 3x 3x da der emiteri erene 2 2 3 1 2 Augmented display 2 2 3 1 3 Data sets importation 2 2 3 2 Data set animation widget o aooo a 22 3 2 1 Animatio
17. Systrip User Manual 29 29 3 5 2 Public house See http biowarehouse ai sri com PublicHouseOverview html for more information on Public house To connect Systrip to Public House you need to use your own login and password To search in the database the name of your network must match with an existing organism in Public House The configuration parameters for this database are as following host the host of the database port the port for the connection e database the database name to query user the user name password the password for the user 3 6 Adding new algorithms As it s based on the Tulip framework user can easily implements it s own algorithms to use in Systrip To know more how to cre ate new plug ins see the Tulip developer manual http tulip labri fr TulipDrupal q developer handbook chapter 6 Plug ins development
18. The time series are mapped along the horizontal axis and values along the vertical axis Figure 2 17 Curve sample 2 2 3 1 3 Data sets importation At this time data sets can be created only from CSV files Values can be organized in row or column but the first value of the list must be the element id The next widget Figure 2 18 is used to turn CSV file into data set Systrip User Manual 16 29 Import data set Use first row as property name Properties Preview sbmlID GMS227 A II GMS227 B Il GMS224 A II GMS224 B Il GMS225 A Il GMS225 B Il GMS226 A Il GMS226 B 1 UREA 188137 211619 333481 315928 234757 229110 244940 256897 2 CPD 6082 21767157 25009216 26480666 24898391 24003818 24467654 27027978 24752181 LACTALD 20284 21066 16396 12503 27345 23901 10389 11624 20284 21066 16396 12503 27345 23901 10389 11624 9502121 10220226 12170409 11265508 11182792 11281498 10972433 10996280 Figure 2 18 Data sets creation widget from CSV file Here is a description for each element of this widget Filename this field must contain the csv file to load Separator this field contains the separator of the CSV file Use first row or column as time series names if checked the first row or column if data are organized in column is treated as labels for loaded time series If unchecked the time series name are automatically generated Properties this list allows you t
19. along a circle Size this sub menu is populated by size algorithms which allow to compute the size of the graph elements General this sub menu is populated by more general algorithms for computing properties subgraphs quotient graphs groups For example the Equal Value algorithm create subgraphs for which the included elements have the same value for a choosed metric property Information this menu contains all the external database operations Display information for selected nodes query databases for each selected node Clean information view clean the information view this option does not erase the downloaded data Clear collected information clean the information view and erase the downloaded data Edit database priority edit the query order for external databases Database properties this menu allows user to edit parameters for each external databases Windows this menu contains two options for the management of the views in the workspace Cascade Arranges all the child windows in a cascade pattern Tile Arranges all child windows in a tile pattern Help in this menu you can find information about the software and plug ins management options See the Tulip documen tation for more information on it 2 1 2 Menu tool bar This tool bar contains 7 shortcut GG Figure 2 3 Menu tool bar al Open Ctrl O open a previously saved Systrip
20. ate zoom zoom and pan Translation is the default operation and can also be activated using the Arrow keys rotation is activated using Shift key zoom is activated using Ctrl key Alt key on Mac zoom and pan is activated using the wheel of the mouse APPLE key on Mac Warning the last operation is mouse position centered i e it attempts to translate the last 2D or 3D position of the mouse to the center of the view Systrip User Manual 20 29 Rectangle Selection Allows multiple elements selection Elements within the selection box are selected If Shift key is pressed the newly selected elements are added to the current selection if Ctrl key Alt key on Mac is pressed the selected elements are removed from the current selection else they replace the current selection 25 Selection edition This tool allows to modify the current selection Available operations horizontal stretch vertical stretch all axis stretch coordinate axis rotation and translation If no key is pressed coordinates are modified If Shift key is pressed only coordinates are modified If Ctrl is pressed only size is modified A left button click outside the selection box reset the selection Press on this circle to rotate the selection ili 4 The square is used both for resizing AND rotating the selection Press on this triangle to change width or height of the selection i Edit edge bends when
21. ations widgets differs for each views and interactors so it s impossible to describe each To know how to configure each view and interactors show their manual 2 2 4 2 Video recorder configuration widget Systrip allows to record video from a view This widget is used to configure the record options see Section 3 4 to know how to record video from Systrip Output directory Browse Frames name prefix Img 4 Force timestamp interval 25 Start Figure 2 21 Output directory the repertory to store temporary screenshots Frames name prefix the prefix for temporary screenshots names e Force timestamp interval if checked ignore the real time before two timestamps and set the value in the spin box as interval time The value in the spin box is in millisecond e Start Stop begin or stop recording video from selected window 2 3 Views 2 3 1 Metabolic view This view is used to display networks drawings It can display graph in two or three dimensions and enables to apply the mouse operations selected in the tool bar by directly clicking on the drawing of the graph 2 3 1 1 View operations 0 of dn WS IK ei D This toolbar allows to select the mouse operation you want to perform Op erations are listed and explained from left to right of the toolbar G 3D Navigation This tool enables the 3D navigation in a graph using the mouse movements left button pressed the available operations are translate rot
22. d Compound Compound 13 29 This widget is responsible of all the data set management operations The Data sets list widget is the main component it displays the list of loaded data sets User can expand each data set to show their elements The Data set properties widget is used to list the properties of each data sets By double clicking on a data set in the list the user can animate them This action allow to use animation on data set see Section 2 2 3 2 for more information on data set animation Only one data set can be animated at the same time 2 2 3 1 1 Contextual menu By a right mouse button press on Data sets list widget user can call the contextual menu It can be different if user call it on an element or not If an element is under the cursor when user right click element s special options are added to the menu Systrip User Manual 14 29 Select Deselect Glyphs gt Delete Import new data set Delete all data sets Figure 2 14 Data set widget contextual menu Select Deselect only visible when clicking on a data set element All elements if all the elements of the data set are unselected or partially selected select them else unselect them Most changing elements select or unselect only the most changing elements of the data set elements with the greatest variation between each time When clicking on it a dialog is shown querying the number of elements to select If all these
23. de called Unclassified elements regroup all the elements that don t belong to any pathway Each node has fields to add information on the element it represents Here is the list of the fields with a description Id the id of the element For pathways Id and Name fields are the same Name the name of the element Type this field give the type of the element There is three types of items pathway compound and reaction Nodes filled only for pathway items Give the number of nodes for the pathway If there is selected nodes in the pathway their number is append between brackets Edges filled only for pathway items Give the number of edges for the pathway If there is selected edges in the pathway their number is append between brackets User can create pathways from the contextual menu Each new pathway must have unique name Once created user can fill it with existing elements To add an element just drag and drop it on the pathway to add it Actually user can only drag and drop compounds or reactions Systrip User Manual Leishmania major Modes 1040 Edges 1062 Id b NAD NADH phosphorylation and dephosp b spermidine biosynthesis b putrescine biosynthesis 111 sulfate activation for sulfonation SULFATE gt spermine biosynthesis New pathway SULFATE Name NAD NADH spermidine putrescine b sulfate activ ATP Sulfate ade sulfate adenosine 5
24. el Coordinates B X 455 64 52 100 60 8 49 4 95 55 Ry 4115 57 6 46 8 91 1 389 75 54 4 44 2 86 65 368 51 2 416 82 2 346 25 a 39 77 75 324 5 44 8 36 4 73 3 302 75 41 6 33 8 68 85 281 38 4 31 2 64 4 259 25 35 2 28 6 59 95 237 5 32 26 55 5 215 75 28 8 23 4 51 05 19 256 20 8 46 6 172 25 22 4 18 2 42 15 150 5 19 2 15 6 37 7 128 75 13 33 25 107 12 8 10 4 28 8 85 25 9 6 7 8 24 35 63 5 6 4 5 2 19 9 41 75 3 2 2 6 15 45 20 0 0 m 5 95 eg payed Figure 2 24 Parallel coordinates view example For more information see the Tulip documentation section 2 5 Tulip documentation can be found here http tulip labri fr userHandbook 2 3 4 2 Table view This view allow to visualize graph properties in a table form Table view unnamed_1 Nodes Edges Fa 42 seam o mms o6 0 0 0 255 153 153 10 C 45 000 255 136 136 11 C m 2 un 00 0255 o 170 170 85 C ts FE 000 255 119 119 13 C 50 0 0 0 255 136 136 11 51 l 00 0 253 0 187 187 68 SCH a xr Figure 2 25 Table view example For more information see the Tulip documentation section 2 5 Tulip documentation can be found here http tulip labri fr userHandbook 2 3 4 3 Histogram view This view plug in allows to create frequency histograms from graph properties supported types are Metric and Integer
25. etabolic view just drag and drop a metabolic view item from the metabolic view widget to the workspace To redraw an existing visualization select its windows and click on the redraw button in the Menu tool bar oron the Redraw current view action in Metabolic network menu The configuration process for visualization is very simple just choose the layout to use To help user to choose the layout a dialog shows the list of all the layout available If you choose a layout in the combo box the system searches if a preview for this layout is available and displays it Metabolic network view wizard Choose the layout to use FM3 Layout fast Figure 3 1 Metabolic representation configuration dialog Systrip User Manual 26 29 Click on Finish button to launch visualization creation process 3 2 Data set visualization creation User can create various representations of data sets To create a new representation of a data set drag and drop a data set from the data set list to the workspace Data sets list Id Name datalsabelMappedTrypanoSanger 3ppm modified csv datalsabelMappedTrypanoSanger 3ppm modified csv Import new data set Figure 3 2 Data set representation creation wizard will appear to show you the available representations There are 3 kinds of representation e Parallel coordinates Histogram e Table Choose the kind of view you want to use This wizard will hel
26. his preview To see the detailed mode for a preview user add to double click on it In the detailed mode the user can interact with a real HTML page This page contains all the information found on the element in the databases User can go back to the preview mode by clicking on the Go back button at the top of the view User can also click on a HTML link in the page to follow them 2 3 2 2 Contextual menu There is only contextual menu on preview screen Save picture as take a snapshot of the view and save it in the selected format 2 3 2 3 Configuration widget Systrip automatically configure this view so you don t need to modify these parameters Systrip User Manual 22 29 2 3 3 Molecular view This view is used to visualize 3D molecules glycerol Figure 2 23 Molecular view sample 2 3 3 1 Contextual menu e Start Stop auto rotate start or stop the automatic rotation of the molecule Rotation Axis select the rotation axis for automatic rotation Center view center the view e Save picture as take a snapshot of the view and save it in the selected format Dialog display or hide the 3D overview 2 3 4 Data sets views These views are used to represent data sets They are specialized to visualize data evolution 2 3 4 1 Parallel coordinates view Parallel coordinates is a common way of visualizing high dimensional geometry and analyzing multivariate data Systrip User Manual 23 29 Parall
27. i Sek Lan cd Sens 1 i curb sr ru Raten F3 251 FSI 300321 RE SCH 201324 BOIS biet nox exa prt icni hanert prazartas Dads Sats Figure 2 1 Decomposition of the Systrip graphical user interface Each part corresponds to a section Systrip User Manual 2 1 2 1 3 29 Menu bar and menu tool bar Hle Edit Metabolic Network Information Windows Help a m amp 5 Figure 2 2 Menu menu tool 1 Menu bar File this menu is used for usual file operations New Ctrl N create a new Systrip perspective Multiple perspective can be opened at the same time Open Ctrl4 O open a saved Systrip perspective Save Ctrl S save the current perspective If there is an older one save overwrites with new data Save As Ctrl Shift S save the current state in a new file Print Ctrl P Exit Ctrl Q Import this sub menu is populated by import plug ins You don t need to use this menu for Systrip Export this sub menu is populated by export plug ins allowing to save a tulip graph accordingly to a specified format By default Tulip is able to export in GML and TLP formats You don t need to use this menu for Systrip Edit Clear selection deselect all selected elements Search in this sub menu allows to search elements in the graph All elements Ctrl F search for elements in the full graph Compounds search for elements in the compounds Reactions search
28. lic network navigation widget The metabolic network is the set of biochemical reactions that occur in a living system Each reaction transforms a set of molecules or metabolites called substrates into other molecules called products In Systrip reactions and molecules are repre sented by nodes a reaction is linked to a molecule only if this reaction consumes or products this molecule Networks can be divided in smaller parts called metabolic pathways Like in the network pathways are composed of reactions and substrates Different pathways can have overlapping sets of reactions and pathways but each pathway must have a unique name Another important feature of Systrip is the capability to create a copy of the full network or of a sub part of it and work with them without altering the original data These copies are called metabolic views When designing Systrip tool we tried to find an intuitive data and views management and used an analogy to book reading when reading a book one usually does not write in it but prefer to use a sheet of paper or a draft This helps to summarize the section s one has read or to play with ones ideas in order to find new insights without damaging the book itself In Systrip the user can therefore use one or several drafts corresponding in our case to views on sub networks of interest The link between each metabolic view and its network is one way Modifications in a metabolic view don t affect network but conver
29. metabolic view widget 9 2 9 Metabolic view name selection dialog 9 2 10 Metabolic view selection example ss ecce X Gs 03 OX RO eee ee ECE GRE REESE X ox ws 10 2 11 Elements display 1 10 2 12 Default properties for the Malate dehydrogenase 11 2 13 Data sets management widget 13 2 14 Data set widget contextual menu 14 Z4 Hab MD a x43 bum Ao RURUR RR mex RAR REED es 15 2 16 Heat map colour mapping 15 2 17 Are sample uocem x ae AE a e aa PNE RR 15 2 18 Data sets creation widget from CSV 16 2 19 Animation properties widget 17 2 20 Animation control widget 18 22 wh eee oa were BBE Gee E BORN ee oe eee Boe oe ee wee ee ES 19 2 22 Information view two state preview and detailed mode 21 2 23 Molecular view 22 2 24 Parallel coordinates view example 23 2 25 able VIEW mou 6 4 Um EG WIR x Eu ib Eee Rb ON EM P SR WU m
30. n Systrip don t be surprised if animation or navigation are affected during recording User can configure advanced options for recording with the Video recorder configuration widget see Section 2 2 4 2 These options cannot be changed during recording To start recording there are two possibilities first you can use the record shortcut in the menu e The second solution is to switch to advanced mode to go to the video recorder configuration widget and to click on the start button see Section 2 2 4 2 If there are no windows selected or if the selected windows cannot be recorded these two controls are disabled When beginning to record a dialog warns user about the possible loss of performance Click on Don t show again to disable this dialog for next video recording or on Ok to just close it Now manipulate Systrip as you want the recording process is running To stop recording click again on the record shortcut or on the stop button in the video recorder configuration widget If frames where captured a file selection dialog will appear to let you choose the video file to create Clicking on the Ok button will launch the video generation and progress bar appear to indicate the progression of the video generation If user click on the Cancel button the video generation will be stopped Systrip User Manual 28 29 3 5 Query more information in distant databases Systrip allows user to get more detailed information from distant database To quer
31. n properties widget 2 2 3 2 2 Animation control widget eee eee eee ee 2 2 4 Advanced options 1 2 2 4 1 View and view tool configuration widgets 2 2 4 2 Video recorder configuration widget 2 5 NI CEET Zo Metabole Vi W A a 6184 Se E owe eee E el bl ee xy Ee E e EH ALL Ta te CEET EENHEETEN 23 112 ss s sce semada tada adaa a RO EC RO EE 224 9 Xonnsuradol WId9eL 2 se Gye ew e FOX ERSGOESXS4X 5 3 Systrip User Manual iv 2 5 2 TEO VIEW ac oca 6 ucc ow eh p Ue od deu eo SA Ewe ee EO 2 3 2 1 View operations 2i 2 5 2 2 Comermal Menis 21 25 2 9 Widget ss wl oo wie Ghee eae SPREE Eee 24 2 3 3 22 2 0 9002 Comekmal Menis sea ka m om dE ow ro hb WO A UE A oho KERES 22 254 Dalasc Views 42658 so ee ox Wow adeo C Ue Rr ode e oe ee A od n eee R 2 3 4 1 Parallel coordinates view 22 E E JODIE VIO 42s oe oe E Orr m eee ow e REUS NA NUR EIE S eS A RS ERE dS S3 23 234 3 Histogramm View se A eee ea X RR Re ee eo Eee EES Ree he a OH 23 2 4 Preferences didlOD s os eoo Rodeo do Xo RR
32. nimation time xoints ms 2000 Hp Size lt gt New mapping creation Mappings Recompute mapping Figure 2 19 Animation properties widget Mapping type define if the mapping for a node is computed only from its own values Local or from all the values of the data set Global Animation time the animation time between two time points in millisecond New mapping creation use the combobox to select the kind of mapping element you want to add and click on the add button There is two kind of mappings size and color mapping e Mappings this is list of mapping elements To delete a mapping element click on its red cross button Each mapping can be edited If the background of an element appears in red it means this element has changed and the whole mapping need to be recomputed to take in account modification e Recompute mapping ifamapping is just created edited or deleted mappings need to be recomputed take modification in accounts Click on this button to recompute mapping If mapping don t need to be recomputed this button is disabled To validate modifications press the apply button Systrip User Manual 18 29 2 2 3 2 2 Animation control widget This widget controls the animation User can start stop or change the current time stamp from this widget Current time point Current time point I GMS224 A Time point selection slide bar Animation control buttons Reset Vie
33. o configure the properties you want to import You can edit the property name or choose if you want to import the property by checking or unchecking the checkbox over the property name Preview this widget just gives a preview of the csv file If a property is not imported it will appear in gray in this preview widget Once the widget fields are filled with the right values click on the Ok button to launch the data set importation Data sets name are generated from the name of the file loaded If you try to load a file with the same name with an existing data set this dialog will appear A dataset with the same name already exist do you want to replace it Cancel Rename Replace Cancel cancel the import Rename change the name of the new data set and import them e Replace delete the existing data set and import the new one Systrip User Manual 17 29 2 2 3 2 Data set animation widget This widget is responsible for data sets animation User can animate nodes size from in function of the current time point value Nodes are growing or shrinking in function of their data from the different time series 2 2 3 2 1 Animation properties widget This widget controls all the animations parameters Only visible in advanced mode it allows to configure the animation parameters like the time of animation or the mapping parameters Animation Properties Mapping type Animation time between two time A
34. p you to choose a view e Table view 2 Histogram view O Parallel Coordinates view Back Next gt Cancel Figure 3 3 View type selection screen Systrip User Manual 27 29 See Section 2 3 4 for more detail on these representations Once the view type selected a screen with the time points to use appear By default all the time points are selected Properties to visualize To GM5225 A ll GMS225 B T I GMS226 A ll GMS226 B ll GMS227_A ll GMS227 B I A A Select all Unselect all Figure 3 4 Time points selection screen Click on the finish button to create the representation 3 3 Find tools The tool gives a way to choose the desired property and the action you want perform regarding the current selection Make out of the found elements a new selection Add them to the selection Remove them from the selection or Intersect them with the current selection You can search elements in the global network or just on a specific kind of element reactions compounds or pathway To search in a specific type select the right menu in the Edit Search in menu If you use the shortcut the elements are searched in the full network 3 4 Register video from view Systrip allow user to make video from a selected window Only one window can be recorded at the same time and it s not possible to change the recorded window during recording Registering video slow dow
35. pound 3 NA Kructose bisphgsphate aldolase NA Reaction A De malate Compound NA an N acykL amino acid NA D isocitrate Isocitrate de Reaction oxaloacetate Compound Aconitate h Reaction succinate Compound P glycolysis glycolysis I Pathway 20 21 a cis 2 enoyl CoA rib flavin trans 3 amp 039 hydroxycotinine NA tiglyl CoA D glyceraldehyde 3 phosphate Triosephiosphatelisomerase gt gluconeo gluconeoge Pathway 21 Elle Views pyruvate id Name dna Noj B Parallel Coordinates view datalsabelMappedTrypanoSanger 3ppm modified csv Dsg ei Information View TCA cycle reachable subgraph gt glycolysis TCA cy View glycoly Pathway co Back m 1 111 I I it i i gt Unclassified elements 20 H H HH E Klee COMPOUND C00158 Help C00158 Compound All links Citrate ere Ontology 1 Citric acid mE KEGG BRITE 1 2 Hydroxy 1 2 3 propanetricarboxylic acid Pathway 4706 4 Display pathways 4 Display compounds W Display reactions amp All Elements Selected Elements Network Navigation Element properties Data Sets 1 See Tulip documentation web page 2 Hydroxytricarballylic acid C6H807 192 027 HO OHO KO HO 27 O OH C00158 Mol file J file DB search Jmol KegDraw Same as 000037 BRITE hierarchy R00351 R00352 R00362 R01322 R01323 R01324 R01325 KEGG
36. row of buttons is the type filter It allow to choose which kind of elements to display e Display pathways if checked display the pathways elements If unchecked all the elements of the network of the view are displayed in the root elements e Display compounds display the compounds elements e Display reactions display the reactions elements The second buttons row allows to filter elements according to their selection state User can display all the elements or only the selected elements When displaying selected elements only selected reactions and compounds are displayed for pathway items only pathways containing selected compounds or reactions are displayed 2 2 2 Elements properties widget This widget displays graph properties for an element When a user query information for a node this widget is automatically shown and a selection of properties are display with their values Only one node can be displayed at a time The element type and its name is displayed at the top of the widget User cannot change properties values Reaction Malate dehydrogenase ld Property Id MALATE DEH R XN name Malate dehydrogenase gluconeogenesis subsystem aspartate degradation Il TCA cycle reversible true listOfReactants Malate listOfProducts oxaloacetate Figure 2 12 Default properties for the Malate dehydrogenase reaction You can set the properties list to display for compounds or reactions in the Information table tab of the preference
37. s Edge size the size or size factor if Use edge size interpolation parameter is checked for edges e Edge extremities size the size or size factoraf Use edge size interpolation parameter is checked for edge extremities 2 4 2 Information Table Reaction properties the list of properties to display in the Element properties widget when displaying infor mation for reactions Compound properties the list of properties to display in the Element properties widget when displaying infor mation for compounds e Query distant databases if checked query distant database when user display information on elements 2 4 3 Metabolic plug ins list This tab allow user to select available plug ins for simple mode see Section 2 1 1 for more information on plug ins Plug ins are organized by type to see the plug in list for a given type just select this type in the combo box at the top of the widget If you want to save the current list just click on the Set as default button If you want to restore original selection click on theRestore default button Systrip User Manual 25 29 Chapter 3 Features 3 1 Network or metabolic views visualization User can create visualization for both of metabolic network and metabolic views There are two different cases creating a new visualization and redrawing an existing visualization To create a representation of the metabolic network just click on the draw metabolic network button For a m
38. s dialog see preferences dialog section Section 2 4 2 2 3 Data sets widget Systrip allows to import and visualize time series expression data on metabolic network nodes From this widget user can perform all the possible operations on data sets It can be divided in two separate widgets with distinct functionality Data sets management widget and Data set animation widget Systrip User Manual 12 29 Info Editor D i Available Data Sets datalsabelMappedTrypanosanger modified csv Data sets management widget Import new data set gt Current dataset properties Animation controller Current Properties I GMS224 Data set animation widget I I I I I DH e Reset View Network Navigation Element properties Data Sets Systrip User Manual 2 2 3 1 Data sets management widget Data sets list datalsabelMappedTypanosanger 3ppm_modifed csv Data set properties GMS224 A GMS224 B GMS225 A GMS225 B GMS226 A l GMS226 B GMS227 A ll GMS227 B Import new data set Name D glycerald N N dimethy 3 hydroxy L L alanine L methionine L leucine anthranilate L glutamate phosphoryl amp amnp alpha sn glycerol D glucosami fructose 6 p dihydroxy a homoserine Figure 2 13 Data sets management widget Compound Compound Compound Compound Compound Compound Compound Compound Compound Compound Compound Compound Compoun
39. selection dialog To add element in an existing view just drag and drop it on the metabolic view name If the element don t exists in the metabolic view it will be automatically added To delete a view user can either use the contextual menu or press the Del or Backspace key When destructing a metabolic network view all it s modification are lost and all the widget related to it s view are closed User can focus on a specific metabolic view by double clicking on it in the metabolic view widget A small icon appear next to the selected metabolic view Once selected the network color is updated to highlight the selected network view To deselect a metabolic view double click on it Systrip User Manual 10 29 File Edit Metabolic Network Information Windows Help mE CR BAL ed Info Editor EEN fomej ubois workepace 3 3 IKestitetaMap tp d Leishmania major EN Leishmania major D x 2 Nodes 1040 Edges 1062 Di Id Name Type Nodes Edc Methylenstetrahydrofolate dehydrogenase NADP aerobicr aerobic resp Pathway 8 6 Ga gt aerobic aerobic resp Pathway 3 2 i sphate 2 5 didehydrogluconat reductase b TCA cycle cycle Pathway 14 12 b glycolysis glycolysis Pathway 20 21 b gluconeo gluconeoge Pathway 21 19 b coenzym coenzyme A Pathway 13 11 f b pentose pentose pho Pathway 14 12 glycoprotein N acetyl D glucgsamirfyl r b pentose pentose pho
40. sely modifying network elements or pathways will affect each view containing these pathways or elements This relation allows to work with metabolic views without altering original and to easily revert modifications Both full network and metabolic views can be draw in Systrip each with a specific representation There are several drawings methods in Systrip for more information about network and metabolic views drawing see Section 3 1 Systrip User Manual 6 29 2 2 1 1 Metabolic network widget This widget is used to visualize and edit metabolic network The next picture describes its interface Redraw network Network name baen Network Leishmania major nodes and Nodes 1040 Edges edges nubmber 1062 Name Type gt aerobic aerobic resp Pathway gt aerobic aerobic resp Pathway TCA cycle TCA cycle Pathway citrate Compound Citrate si 5 Reaction amp amp alpha Compound Network Succinate d Reaction elements Malate dehy Reaction cis aconitate Compound fumarate Compound D isocitrate Compound NA Reaction malate Compound Isocitrate de Reaction oxaloacetate Compound Aconitate h Reaction succinate Compound b glycolysis glycolysis Pathway gt gluconeo gluconeoge Pathway Figure 2 5 Metabolic network widget interface description Networks are represented as a tree pathways are inner nodes containing a leaf node for each reaction and compound The specific no
41. sfying some criteria Systrip User Manual 4 29 Algorithms only visible in advanced graphical mode This menu apply algorithms on the selected network view or on the full network if no one is selected It is divided in several parts to make a difference between the kind of algorithms you can apply For more information please visit the Tulip documentation on algorithms section 3 2 and graph properties section 3 3 Selection this sub menu is populated by selection algorithms These algorithms allows to select nodes and or edges satisfying some criteria For example the Loop Selection algorithm detects all edges for which the starting and ending nodes are the same Color this sub menu is populated by color algorithms These king of algorithm computes the color of the graph elements A default one Metric Mapping is provided it allows to color all graph elements according to a metric property Measure this sub menu is populated by metric algorithms These algorithms allow to compute and assign a value to the viewMetric property of graph elements For example when running the Degree algorithm the degree the number of its neighbors is computed and assigned to each graph node viewMetric property Layout this sub menu is populated by layout algorithms which allow to display graphs using different types of drawings For example the Circular algorithm places all nodes of a graph
42. w Figure 2 20 Animation control widget Current time point the Current time point label displays the name of the current time point and the LCD screen displays his index e Time point selection slide bar allow user to easily jump to a given time point Move the cursor to jump directly to the selected time point e Animation control buttons e jump to the previous time point bct D launch the animation from the current time point to the last To stop animation click on the pause or on the stop button lll stop animation but keep the current time point position stop the animation if started and go to the first time point If animation is not running jump to the first time point ig i E A jump to the next time point Reset view reset the visual parameters 2 2 4 Advanced options widget This widget is only visible when advanced mode is enabled see Advanced mode in Edit menu It allow user to access to view view tool and video recorder configuration widget Systrip User Manual 19 29 2 2 4 1 View and view tool configuration widgets These widgets are used to configure respectively the selected view and selected view interaction tool When user change the selected view or the selected view tool they are automatically updated If no configuration widget is available for a given view or view interaction tool a description widget is displayed Configur
43. work manipulation layer on top of it Such 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 Systrip features as Systrip is based on the Tulip library you can find more detailed information on Tulip documentation File Edit Metabolic Network Information Windows Help e loce mm 3 7 3 Info Editor 1 amp home jdubois workspace Tulip 3 3 1 Tryp tlp Leishmania major Leishmania major Nodes 1040 Edges 1062 TCA cycle reachable subgraph Id Name Type Nodes Edc gt aerobicr aerobic resp Pathway 8 6 P aerobicr aerobic resp Pathway 3 2 TCA cycle TCA cycle Pathway 14 12 amp amp beta D glucose 6 phosphate CIT citrate Citrate si s Reaction Compound T acyl glycerone 3 phosphate amp amp alpha Compound Succinate d Reaction Malate dehy Reaction cis aconitate Compound N N deetyl D ghic samine alditol guanine N ProteinsfarrifeSyltransferase Glucose 64phogphate isomerase malate oxaloacetate fructosp 6 phips phate fumarate Compound d citrate D isocitrate Com
44. y information on an element use the element information interactor or right click on the element in the metabolic network widget or metabolic view widget and select the Show properties action The information retrieval process is as follows take the first database in the list and try to find the element if no element is found go to the next database until the element is found or all the available database are queried User can edit the database query list to add remove databases or change the query order To edit this list use the Edit data base priority action in the Information menu widget will appear to help you to edit the list Edit database priority Unselected Databases Selected Databases PublicHouseQuerrier KEGG Querrier Select all Unselect all e Cancel Figure 3 5 Database priority edition widget move unselected database to selected database list i move selected database to unselected database list T increase the priority of the selected database I decrease the priority of the selected database e Select all select all the database e Unselect all deselect all the database Each database has their own parameters user can edit them for a given database by selecting the database name in the Database properties menu 3 5 1 KEGG See http www genome jp kegg for more information on KEGG There is no configuration parameters for this database
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