ProteoLens in - Discovery Informatics and Computing Group
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1. KRAS Bladder_cancer RB1 Bladder_cancer HRAS Breast_cancer CHEK2 Breast_cancer PIK3CA Pancreati1c_cancer RBBP8 Renal_cell_carcinoma FLCN Renal_cell_carcinoma RNF139 Renal_cell_carcinoma OGG1 Renal_cell_carcinoma PRCC Renal_cell carcinoma TFE3 Renal_cell_carcinoma MET Renal_cell_carcinoma VHL Stomach_cancer KRAS Optional Installing and Configuring Oracle XE A principal advantage of ProteoLens is how it directly connects with a database To help you get started brief instructions are provided here for downloading and installing Oracle XE a free basic entry level database This optional step of installing Oracle XE is a task separate from but strongly complementary to the 10 minute tour in this guide Oracle XE can be downloaded from http www oracle com technolo roducts database xe index html You will want to install from the OracleXE exe or the OracleXEUniv exe file You will need to specify three parameters during the installation The values used for the examples in this manual are indicated 1 Destination Folder C oraclexe 2 HTTP Listener Port 8081 3 System administrator password for both SYS and SYSTEM your choice Note the database SID db_name for OracleXE is set to XE by default Viewing the database A default installation of Oracle XE places the application Oracle Database 10g Express Edition in your main start menu list of programs Selecting the Oracle Database menu item provides you w2. and select View from the submenu see Figure 5 The next major section of this manual will describe how you convert the resulting view into a data association ProteoLens Integrated System Biology Platform File Window DataManagement Help gt c HA t Ed XE amp EI ANONYMOUS L CTXSYS amp CI DBSNMP amp ci DIP amp cI FLOWS 020100 I FLOWS_FILES gt JHR 1 MDSYS o CI MYTESTUSER and Collapse Figure 5 Using the ProteoLens interface to select a table object from an OracleXE database Connecting to File based Input You may choose to skip this step since the rest of the tutorial exercise relies on the database input connection Navigate to a file with the Filesystems window For purposes of this example you can use the example gene_disease txt file bundled with the ProteoLens installation Right click on the file that contains data you wish to input into ProteoLens and a submenu will emerge as shown in Figure 6 Click on the Table data check box Then select the View option from the submenu ProteoLens Integrated System Biology Platform File Window Data Management Help o E ProteoLens Org 9 EI ProteoLens J class E doc E examples gene_diseas gt c3 lib Expand ProteoLensi1 0 g Collapse h ProteoLens 1 0 1 README tet F Table data history txt a license rtf MME Figure 6 Using a Filesystems submenu to view the table data of a file A window then ap
3. E Een perth H E ANONYMOUS Hselect from MYTESTUSER GENEDISEASETABLE o EI cTxsys gt CI DBSNMP cF DIP o c FLOWS 020100 o EJ FLOWS_FILES CHR EI MDSYS Ie EE MYTESTUSER Bladd Tyg Ee DISEASE GENE_SYM Figure 8 Creating a data association part 1 O x Filesystems FIG gt FH E XE gt EJ ANONYMOUS o E CTXSYS amp DBSNMP o ES DIP 4 FLOWS_020100 J SYM amp EI FLOWS_FILES Input Data Association name o ES HR gt E Mpsys genediseas Gd MYTESTUSER 2 GENEDISEASETA ea ereastcan_PIRaCa Meese ose mmea Mi o a bd pT TUSER GENEDISEASETABLE Memory 62 50 508 Figure 9 Creating a data association part 2 A special note about data associations Data associations in ProteoLens are the architectural layer that wraps external data from flat files or database tables in a uniform way Importantly as described in the user manual The ProteoLens application makes no domain specific assumptions about the nature and meaning of the provided data which leaves the user with responsibility of using right data at the right place but also allows for very high flexibility As will be described in the next section data associations can be used for either visualization or annotation Viewing and Annotating a Network Visualizations and annotations are created from data associations A visualization is the graphical layout of
4. F1 les IUPUI ProteoLens_1 1 1 examples gene_disease txt REPLACE INTO TABLE GENEDISEASETABLE FIELDS TERMINATED BY x 09 OPTIONALLY ENCLOSED BY TRAILING NULLCOLS DISEASE_NAME GENE_SYMBOL After you have created the table structure for GENEDISEASETABLE open a Windows command prompt and type the following sql ldr control Cc Program Fi les IUPUI ProteoLens_1 1 1 examples gene_disease_load ct After entering this command you will be prompted to enter the appropriate username e g MYTESTUSER and password Connecting to Database and File based Input When using ProteoLens the general form of input is either a two or three column relational format In the ProteoLens user application this form of input can be accessed from either a flat file or a supported database type Supported database types are Oracle and PostgreSQL Databases can be accessed across the network or hosted on the same computer running the ProteoLens application The advantage of connecting to a database for input is that you can quickly iterate through different relational associations based on sending SQL queries from the ProteoLens interface directly to the backend database A connection begins with using the Filesystems window and viewing a file or database object right click with mouse It is at this point of the manual that the 10 minute exercise begins This exercise assumes that you have installed Oracle XE on your system with a user named MYTEST
5. ProteoLens A Biological Network Visual Data Exploration Annotation and Data Mining Tool FOR PROTEOLENS VERSION 1 1 DOCUMENT LAST MODIFIED NOVEMBER 2008 select ADISEASE NAME DISEASE_A B DISEASE_NAME DISEASE_B count B DISEASE_NAME NUMLINKS from MYDATABASE GENEDISEASETABLE a MYDATABASE GENEDISEASETABLE b where a GENE_SYMBOL B GENE_SYMBOL and DISEASE_NAME lt B DISEASE_NAME group by ADISEASE_NAME B DISEASE_NAME DISEASE_A DISEASE_B NUMLINKS Bladder_cancer Breast_cancer Colon_cancer Pancreatic_cancer Breast_cancer Stomach_cancer Bladder_cancer Stomach_cancer select from MYDATABASE GENEDISEASETABLE H ast_cancer Lymphoma ast_cancer Pancreatic_cancer DISEASE_NAME GENE_SYMBOL creatic_cancer Stomach_cancer Bladder_cancer FGFR3 phoma Mesothelioma Bladder_cancer KRAS Bladder_cancer RB1 ider_cancer Colon_cancer Bladder_cancer HRAS ider_cancer Leukemia Breast_cancer CHEK2 emia Lung cancer Breast_cancer PIK3CA st_cancer Ovarian_cancer er noma Pancreatic_cancer Breast_cancer SLC22A18 gatic Breast cancer TP53 _cancer Pancreatic_cancer Breast_cancer BRCA1 kemia Pancreatic_cancer Breast_cancer BRCA2 cancer Stomach_cancer Breast_cancer TSG101 bn cancer Leukemia Breast_cancer BRIP1 bn can
6. USER Connecting to Database Input In order to connect to a database object you must first mount the database To mount the database you need to right click on the root Filesystems node in the Filesystems window and select the Mount database option that appears in the submenu as shown in Figure 3 As shown in Figure 4 use the Thin connection type and enter the parameters as described in the previous section in this manual on installing and configuring Oracle XE ProteoLens Integrated System Biology Platform File Window DataManagement Help Collapse Refresh Mount database lemory 62 47 508 Figure 3 Right clicking on the root level Filesystem node presents the Mount Database option Please specify connection parameters select database type Oracle Select connection type Thin connection 2 OCIS connection requires Oracle client and TNSNAMES ORA Thin connection parameters Database server 127 0 0 1 Database port 1571 Database SID XE User schema parameters Username schema MYTESTUSER Password pessos SSS O _ Save password INSECURE Figure 4 Specifying connection parameters for mounting a database The settings shown are based on a default installation of Oracle XE and the existence of a username MYTESTUSER Use the Filesystem window to navigate to the database named XE open the schema named MYTESTUSER and right click on the table object GENEDISEASETABLE
7. ating a non administration level user Go to the database web interface page e g http 127 0 0 1 8081 apex and after logging in with the SYSTEM user use the Administration link and select the Database Users gt Create User option You may then create a non administration level user from the provided interface as shown in Figure 2 Create Database User Userame MYTESTUSER Password Expire Password Account Status Unlocked Default Tablespace USERS Temporary Tablespace TEMP Roles M CONNECT M RESOURCE DBA Direct Grant System Privileges CREATE DATABASE LINK JT CREATE MATERIALIZED VIEW 7 CREATE PROCEDURE CREATE PUBLIC SYNONYM CREATE ROLE CREATE SEQUENCE T CREATE SYNONYM CREATE TABLE CREATE TRIGGER CREATE TYPE CREATE VIEW Check All Uncheck All Figure 2 Creating a non admuinistration level user for Oracle XE Uploading File based Data with SQL Loader sqlldr You first need to create the table structure you want to load data into Login as MYTESTUSER and through the SQL link on the Oracle XE web application open an SQL command window and enter the following command CREATE TABLE GENEDISEASETABLE C DISEASE_NAME VARCHAR2 100 NOT NULL ENABLE GENE_SYMBOL VARCHAR 100 NOT NULL ENABLE The following file gene_disease_load ctl is provided as an example of loading data from a tab separated file into Oracle XE OPTIONS SKIP 1 LOAD DATA INFILE C Program
8. cer Lymphoma Breast_cancer RAD54L ae CDH1 ast_cancer Melanoma ae a a os a cs Gad es a ce es ce a ee Breast_cancer AR Breast_cancer KRAS Breast_cancer RB1CC1 Breast_cancer PHB Breast_cancer ATM Breast_cancer i BARD1 Breast_cancer RAD51 Breast_cancer XRCC3 Colon_cancer RAD54B Colon_cancer RAD54L Colon_cancer BCL10 Colon_cancer PTPN12 Colon cancer TGFBR2 Your Very Own Quick 10 Minute Guide to Doing Almost Everything Table of Contents INtFOCUCTION TO Proteo LENS anino 1 Getting the ProteOLens SoWalE sinia 1 ESCTONRC ASTAMING aaa earn Geren Gare crea eared ee 1 Installing ProteoLens and Launching the Application ccsseeeen 2 Example Data Diseases and their Genes ccscssssssssssssssssscscscssscsessssseseees 2 Optional Installing and Configuring Oracle XE csssssssssssssssssessseseeseseeeeees 3 Viewing the CAtADASE sssssssssssssssessesssessessssssessesssessesssessessessaessesssesacsssesaesaessaessesseesaeessesaesaeessess 3 Creating a non administration level user Uploading File based Data with SQL Loader SQICr cssscssessssssessesssessesssessessessesseesesees 4 Connecting to Database and File based Input ccssssseseeeeeees 5 Gonheciing 10 Database NOU ea a ans ae eE 5 Connecting to File based INput cccesssesesesssssssssseesescscsesssssssesssessseseess
9. cifying a new edge annotation with the edgecount annotation The resulting annotated disease to disease network is shown in Figure 21 16 Network 5 Current source diseasedisease Network Edit Zoom Layout Find Visualization Filter Fenal_c Figure 21 Final output view of annotated nodes and edges of a disease to disease network The thicker lines represent a greater number of genes in common between the corresponding pair of diseases The enlarged nodes represent those diseases that occur most often in the disease to disease association From Figure 21 we observe that the colon cancer and leukemia have the highest numbers of listed genes and that stomach cancer and mesothelioma have the lowest numbers of listed genes We can also infer that ovarian cancer has a greater percentage of its listed genes in common with colon cancer than the percentage of listed colon cancer genes that are in common with ovarian cancer 17 Managing your Workflow Sessions Saving Export and Printing Options for exporting and printing network views are provided in the Network menu of the Network window as shown in Figure 22 Sessions and Saving From the File menu of the ProteoLens interface you can save your session You can then close ProteoLens and reload your session at a later time Sessions are saved in XML format A saved session contains your working set of data associations and mounted database connections Note that the window layo
10. database free for download and usage Oracle XE can be accessed from http www oracle com technology products database xe index html As an alternative to Oracle XE you can also install and use PostgreSQL with ProteoLens Installing ProteoLens and Launching the Application ProteoLens is released as a standard Windows software installation package After downloading the ProteoLens installation executable double click on the executable and simply click OK to install Figure 1 shows the ProteoLens interface You can navigate both database and file based input choices from the filesystems window as will be described in subsequent sections For visualization a new network window can be opened in the right of the interface through use of the Window menu accessed from the top menu bar of the interface Ey ProteoLens Integrate Ioj x File Window Data Management Help Filesystems Filesystems om FCA amp GAD FF Es O GFA FG O Fy H na omanr ADAA Ane Figure 1 ProteoLens interface This is what a user sees when first launching the ProteoLens application Example Data Diseases and their Genes The ProteoLens application comes with various example data sets In this tutorial guide the file gene_disease txt is a two column tab separated flat file containing content structured in the manner below based on data from Goh e al 2007 DISEASE_NAME GENE_SYMBOL Bladder_cancer FGFR3 Bladder_cancer
11. eeeeeeess 7 The Fine Art of Data ASSOCIATIONS cccccccceseeseeseseesesseeseesesseeseeeeeaees 9 A special note about data ASSOCIATIONS cceeeessssesesesesseseseseesseseseeseenseeseens 10 Viewing and Annotating a NEtWOmm cccccsessssssssessesseseeeseeeeeeeeees 10 Visualization Showing the Network cccscssssssesssssscsssssssssssssssssssseseesesssaees 10 Annotating the INGTON K ais toes va eenatetascts wiaasmves tdasubatncsan ieatshanvasedstavesadnaumastahinceadiaranas 14 Managing your Workflow Sessions Saving Export and Printing 18 DeSsiONS and SAVIN Giiiss tice ea ect eee sti 18 Saving Network Files with GML Files csssssssssssssessssssessesssessessssssessessesseessesaeeaeessesneesseens 18 EXON GUNG FINNO sitorcicecsssctcciuss Seaanssncvecs coaches chess couSacuentechespasssethastivners oe iacaananend 18 Important Notes ON Usage cccccsessesseseessssssesesseseeseeseesaesaesaesessnseneees 19 PROTEOLENS IN 10 MINUTES A QUICK GUIDE Introduction to ProteoLens Installing ProteoLens is a breeze All it requires is a java runtime environment Lo achieve its maximal range of performance you may also want to install the free Oracle XE database application onto your system You are encouraged to print out this guide before getting started iological networks often reveal a wide variety of structures and functions that when constructed for analysis may be used to study t
12. he development and phenotype of organisms A challenge has been to find tools that enable multi scale analyses of biological networks with the right kind of architecture to smoothly and quickly handle diverse types and associations among heterogeneous biological data ProteoLens has been built as a next generation biological network visual data exploration annotation and mining tool It has many advanced features that support expert bioinformaticians to perform large scale network based integrated data analysis This guide has been written to present first time users with an accelerated experience tour through the features and power of ProteoLens This guide assumes installation and usage of ProteoLens on a Windows 95 98 ME 2000 XP Vista operating system For more information you may also want to consult the more extensive user manual available at http bio informatics iuput edu proteolens usermanuall 0 pdf Getting the ProteoLens Software ProteoLens can be downloaded in a ready to install executable from the website http bio informatics iuput edu proteolens Before Installing To run ProteoLens you must have Java Runtime Environment version 1 42 or higher installed on your computer You can get the Java Runtime Environment from http yava sun com In order to complete the 10 minute case study exercise described in the following pages it is also recommended to install Oracle XE on your computer Oracle XE is a basic entry level
13. ion envelope Respect filter _ Connect only Figure 12 Select network source interface From this interface you will need to specify loading conditions using the Condition buttons prior to clicking on the OK button Set condition for subnetwork being loaded _ Available data associations Annotation display editor genedisease Treat data as Filters Search pattern i Applyfilterto originalset current Data association has node IDs in DISEASE GENE_ Sv 2 all accessible L displayed Figure 13 Interface for specifying loading conditions A basic set of steps for using this interface is 1 select genedisease from the list of available data associations upper left 2 highlight all values that appear in the data values window lower right and 3 click the OK button Upon returning to the Select network source interface shown in Figure 12 click the OK button there also After completing the steps of selecting the network source and specifying loading conditions a network view will appear similar to the network shown on the front cover of this instruction manual Note however that as you repeat the exact same procedure the node to node associations will remain the same but the physical layout of the network on the screen will be somewhat random The network shown presents how genes link to each other through association with the same disease To construct a network that connects d
14. iseases directly together based on having a common gene you can substitute with the following SQL when viewing the 12 GENEDISEASETABLE object Figure 5 create a data association and repeat the steps in Figure 12 Figure 13 and Figure 14 SELECT A DISEASE_NAME AA B DISEASE_NAME BB From MYTESTUSER GENEDISEASETABLE a MYTESTUSER GENEDISEASETABLE b where a GENE_SYMBOL B GENE_SYMBOL and A DISEASE_NAME B DISEASE_NAME group by A DISEASE_NAME B DISEASE_NAME The resulting network view based on the substituted SQL is shown in Figure 14 Network 5 Current source diseasedisease Network Edit Zoom Layout Find Wisualization Filter siomgeh_jancer Renaldo reinoma Figure 14 Output view of disease to disease associations shown only with defaults for node and edge annotations 13 Annotating the Network Annotating the network also utilizes data associations For annotating nodes the specified data association takes the form of an ordered pair node_name annotation_value For annotating edges the specified data association takes the form of an ordered triplet where nodel and node2 indicate the edge nodel_name node2_name annotation_value With SQL you can build these annotation tables from your original annotation table without uploading new tables into your database environment Follow the steps described in Figure 8 and Figure 9 and use the SQL commands below to define data associations diseasecount and edgecou
15. ith a link Go to Database Home Page The web interface to Oracle XE is a simple to use interface providing a range of options from administration including the creation and management of non administrative users browsing of database objects such as tables and views creation and launching of SQL scripts and utilities that include options for loading external data into the database system During installation configuration and uploading of content it is important to make note of five basic parameters 1 the database user that has permissions to the content you wish to access from ProteoLens after installation you may ideally wish to create a non administrative level user Oracle XE account for connecting to ProteoLens application you will need to remember the password associated with this account 2 the SID containing content you wish to connect to by default this is set to ce 29 XE 3 the table name with content you wish to access and query from ProteoLens 4 the port number to the Oracle XE application default value is 1521 and 5 the IP address hosting the Oracle XE application this will probably be 127 0 0 1 unless you are installing Oracle XE on a computer separate from the one you are using ProteoLens This manual presumes the following values for connecting to Oracle XE user name MYTESTUSER SID XE table name GENEDISEASETABLE port number 1521 and IP address 127 0 0 1 Cre
16. nodes and edges in the network An annotation is the modification of nodes e g labels sizes colors or edges e g labels line widths colors based on input that links to the identities of the nodes or edges Visualization Showing the Network Visualization starts with opening a network view through the Window menu as shown in Figure 10 10 ProteoLens Integrated System Biology Platform 0 x File Window Data Management Help Figure 10 Opening a new network view In the newly opened Network View window the Load Network from data association option can be used to construct the network based on the uploaded data association see Figure 11 ProteoLens Integrated System Biology Platform File Window DataManagement Help Edit Zoom Layout Find Visualization Filter Load Network from GML file Save as ki Nodes from the ID list Save selection as Save image as Print Close Figure 11 Beginning the process of loading a network from a data association Figure 12 Figure 13 and Figure 14 show the process of selecting the network source specifying loading conditions and recetving the output view respectively To specify loading conditions from the Select network source interface click on either Condition button Figure 12 11 Select network source Fitter data DISEASE_NAME IN LIST ha OR v Synchronize lists GENE_SYMBOL Wust LIST ha Condition _ Load interact
17. nt SQL command for diseasecount SELECT DISEASE_NAME count GENE_SYMBOL m FROM MYTESTUSER GENEDISEASETABLE GROUP BY DISEASE_NAME For annotating edges a 3 column table is specified typically with SQL Typical usage is to have the first two columns specify the identity of each edge and the third value third column is the annotation for that edge Here is an example of building an annotation table for edges with SQL as shown in Figure 15 Figure 16 and Figure 17 SQL command for edgecount SELECT A DISEASE_NAME AA B DISEASE_NAME BB count B DISEASE_NAME M from MYTESTUSER GENEDISEASETABLE a MYTESTUSER GENEDISEASETABLE b where a GENE_SYMBOL B GENE_SYMBOL and A DISEASE_NAME B DISEASE_NAME group by A DISEASE_NAME B DISEASE_NAME l ProteoLens Integrated System Biology Platfors m oO X File Window Data Management Help Filesystems cJ HA E XE gt EJ ANONYMOUS gt cI cTxsys cI DBSNMP J DIP EI FLOWS 020100 CI FLOWS_FILES gt JHR gt cI mpsYS CI MYTESTUSER GENEDISEASETABLE cF OUTLN MYTESTUSER GENEDISEASETABLE File Query Result SELECT A DISEASE_NAME AA B DISEASE_NAME BB I count B DISEASE_NAME M fram MYTESTUSER GENEDISEASETABLE i a MYTESTUSER GENEDISEASETABLE b i where a GENE_SYMBOL B GENE_SYMBOL and H A DISEASE_NAME B DISEASE_NAME group by A DISEASE NAME B DISEASE_NAME Eoo 8 w _ Memory 62 47 508 Figure 15 Creating the edgec
18. ount annotation part 1 14 Select columns to import Input Data Association name edgecount Figure 17 Creating the edgecount annotation part 3 From the Visualization menu in the network view you can choose to Add annotation to either Nodes or Edges as shown in Figure 18 ProteoLens Integrated System Biology Platform File Window Data Management Help Network 3 Current source diseasediseas GI XE Network Edit Zoom Layout Find Wi gt EI ANONYMOUS gt CTXSYS gt CI DBSNMP Edges gt Default gt cI DIP Renal cio i Add annotation o cI FLOWS 020100 Mel Edit annotations EJ FLOWS_FILES T Show direction EJ HR oa gt cJ MDSYS Glioflasipma E MYTESTUSER GENEDISEASETABLE gt EI OUTLN gt cJ sys y EA SYSTEM ovarign_ 9 nicer k TSMSy 5 hidlar emory 62 49 508 Figure 18 Using Visualization menu of a network view to begin the process of adding an annotation 15 Figure 19 and Figure 20 show the specification of a new node annotation and a new edge annotation Create new node annotation schema Annotation display editor Treat dataas Sting v Filters Search pattern sid Applyfitterto original set gt current su oe pattem ss s s siSY Apply fiter to originalset current subset Reset Data association has node ID pairs in AABB M J all accessible displayed Figure 20 Spe
19. pears as shown in Figure 7 and appropriate options are selected For this exercise you should select Tab for the field separator and click on the checkbox for the first row containing column names ProteoLens Integrated System Biology Platform File Window Data Management Help Select field separator E ProteoLens Org Comma Semicolon Tab o ProteoLens gt EJ class J doc First row contains column names w Ei examples pData preview gene_disease tt DISEASE_NAME GENE_SYMBOL 55 lib H Bladder_cancerFGFR3 ProteoLens 1 0 exe Bladder_cancerKRAS ProteoLens 1 0 ini README tet history tet B license mf Figure 7 Previewing flat file data for import into the ProteoLens application After you have completed the View action on your input file the next step would be to create a data association as described in the next section The Fine Art of Data Associations After completing the steps in the previous section you can proceed to make a data association as shown in Figure 8 and Figure 9 For this tutorial guide work with the view that comes from the GENEDISEASETABLE object in the OracleXE database Figure 8 shows the window that appears in the ProteoLens interface after selecting View as shown in Figure 5 E ProteoLens Integrated System Biology Platform File Window Data Management Help I E MYTESTUSER GENEDISEASETA o m Bd E Gi File Query Resul E HA Gl X
20. s used in table names column names and data field values e Use capital characters and underscores for table names and column names e Do not use spaces inside data field values instead of Retinal cell carcinoma use Retinal_cell_carcinoma e Be aware of the 30 character length limitation on table names and column names in Oracle XE e In order to avoid appending spaces to data field values use VARCHAR2 as a column type and not CHAR The example data files in the ProteoLens installation and the contents of this guide are consistent with the above recommendations 19
21. ut is not saved and after restarting your session you will need to regenerate your network views or load them from separately saved GML files Saving Network Files with GML Files Saving and loading of each network view in your session can be done with the standard GML file format see Figure 22 The exact physical layout of the network is preserved Export and Printing The Save image as option allows for exporting the image into jpeg or png graphical file formats ProteoLens Integrated System Biology Platform File Window DataManagement Help Network 1 eye eerie E Filesystems Edit Zoom Layout Find Visualization Filter E EID GEN om GFA FIG Save as H GML file I Save selection as List of node IDs Save image as FHA a cose gt CI ANONYMOUS gt E CTXsYs gt EJ DBSNMP gt E3 DIP gt EI FLOWS 020100 o EI FLOWS_FILES i gt CHR Vo Men L un 4 fa T R E ay Figure 22 Options for saving and printing network views You can also choose the Print option The network view is automatically downscaled as needed to fit the print output medium Note that the zoom level and display window boundaries in the ProteoLens application do not control printing Important Notes on Usage At the time of this writing to ensure the highest amount of compatibility between database and java resources we make the following recommendations for character set
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