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About

Release Notes for

ENTERPRISE BIOLOGY SOFTWARE 2009 (Version 9.0)

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Description of the Software

The Enterprise Biology Software (EBS 2009; Version 9.0) includes:

Systems Biology Two (1.0)
Information Interface (1.0)
Database Upgrades (2009)
Stereology Literature Database
Universal Biology Database

Before you begin, you need:

Software	Enterprise Biology Software 2009; DVD
DVD Drive	To install the program
Processor	Recent Intel or AMD personal computer
RAM	500 MB (minimum) – 1GB of memory (recommended)
Disk space	EBS Software Package 9.0; 412 MB of hard disk space on the C drive
OS	Microsoft Windows 95, 98, 98SE, Me, 2000, NT 4.0, XP, Vista, Windows7
Resolution	1280 by 1024 pixels (right click desktop Properties/Settings)
Display Properties	Appearance tab - set Scheme to Windows Standard
Color Depth	High Color or True Color (recommended)
Font Size	Small

Installation Overview

A relational database is installed in a client/server configuration. The software uses a runtime database engine (rtdsk50.exe) that connects a user interface to a backend server. Many of the database programs employ a “query by example” interface. During the installation, the client/server configuration will be set up automatically on the target computer. The Uninstall program removes all traces of the original installation.

Installation

Install the Universal Biology Database Software (2009) from the DVD

Step 1: Put the EBS 2009 DVD in the center ring (80 mm) ring of the DVD drive, close the door, and the installation starts automatically. Run the installation program.
Step 2: Install Adobe Acrobat Reader 9.3. On the opening screen of the Universal Biology Database (main menu), click on install reader. Follow the directions. If Adobe Acrobat Reader 9.0 is already installed, this step can be skipped.

Troubleshooting the installation

Since the installation is based on the Windows Installer Program, it should be unremarkable.

Problems that do appear most likely will be the result of not setting the resolution (1280 by 1024 pixels), color (High Color or True Color), or font size (Small) as recommended.
The current resolution setting (1280 by 1024 pixels) may exceed that of your monitor and/or graphics card, thereby obscuring command buttons. If so, click on the scroll button – if present.
It is also a good idea during the installation to have no open applications and no applications running in the background (this includes anti-virus software, crash monitoring software, and system diagnostic software).

Uninstall the Universal Biology Database Software

Press the Start button on the toolbar; select Programs, EBS 2009, and Uninstall EBS 2009. This is the recommended procedure. Alternatively, the programs can be removed from the control panel.

Running the Enterprise Biology Software

Starting the Universal Biology Database program

To start the program, double click the EBS 2009 icon or start it from the program list - Start/programs/EBS 2009.

Selecting programs

In the opening screen, select an item in the menu. Adobe Reader 9.0 (or 9.3) must be installed to view the PDF text files. The EBS software uses a hardcoded path for the PDF files: C:\Program Files\Adobe\Acrobat 9.0\Acrobat.exe.

Technical Issues

Program notes

The default paper size for printing is 8.5 x 14 inches (Legal).
A sort button (usually a radio button) often has two functions (left mouse click = ascending; right mouse click = descending or ascending + remove blanks)
Some of the programs are large and may require long loading times, depending on the memory and operating system of the client computer.
When a command button has a thick border, is can be "clicked" by pressing the Enter key.

Known problems

The quality of the display depends importantly on the recommended settings for resolution, color depth, and font size. Most display problems can be fixed by following the directions given above (See: Before you begin…).
Installing the new software (2009) changes the ODBC setting for the main database. This may interfere with earlier EBS programs using the same database. The fix is to reinstall the older program.
If clicking on an accession number does not automatically copy it to the data entry field during an Internet search, highlight the number and use copy (hold down Ctrl press c) and paste (hold down Ctrl press v).
Some computers running the Vista operating system fail to display .pdf files when their buttons are clicked in the EBS programs– even when the Adobe Reader is properly installed. The work around is to find the files in the folder (C:\Program Files\EBS 2009) and double click on them.

ENTERPRISE BIOLOGY SOFTWARE (9.0) 2009/10

INFORMATION INFRASTRUCTURE (1.0)
SYSTEMS BIOLOGY TWO (Version 1.0)

Window Name (as it appears in on the screen)	Program (.exe) or File (.pdf)	Notes
SYSTEMS BIOLOGY TWO	UBD_2009.exe	Enterprise Biology Software 2009/2010
1. Documents		Progress reports
2009	Paper10.pdf	Progress report for 2009
2008	Paper9.pdf	Progress report for 2008
2007	Paper8.pdf	Progress report for 2007
2006	Paper7.pdf	Progress report for 2006
2005	Paper6.pdf	Progress report for 2005
2004	Paper5.pdf	Progress report for 2004
2003	Paper4.pdf	Progress report for 2003
2002	Paper3.pdf	Progress report for 2002
2001B	Paper2.pdf	Progress report for 2001
2001A	Paper1.pdf	Progress report for 2001
Rule book	Rulebook1.pdf	Guidelines for a Quantitative Biology
Forms	Forms_1.pdf	Data entry forms
Read	Read1.pdf	Introduction / Help
2. Software Tree	Info_infra.exe	Information Infrastructure
Stereology Literature Database
Standardize Data
· Data Entry Tools
Graphics to Numbers	Graphics_toolhr.exe	Convert graphs into numbers
Hierarchy templates	Ubd_sort_hierhr.exe	View data input hierarchies
· Enter Data
Citation	Issb_cit.exe	Enter citation data
Citation List	Sort_cit.exe	Display list of citations
Methods	Issb_met.exe	Enter methods data
Control	Issb_co.exe	Enter control data
Lookup Tables	Issb_lookup.exe	Lookup tables for data entry
Print Citation	Elec_e1hr.exe	Standardized paper
Experimental	Issb_ex.exe	Enter experimental data
· View Catalogues
Citation	Ubd_cit_listhr.exe	Find papers by citation et cetera
Citation by Data	Ubd_ui5hr.exe	Find papers by control data
Citation by Method	Ubd_ui3hr.exe	Find papers by methods
Stereology Literature Database - Co	Ubd_sldb_c.exe	Catalogue of stereological data - Co
Stereology Literature Database - Ex	Ubd_sldb_e.exe	Catalogue of stereological data - Ex
Standardized paper - control	Elec_c1hr.exe	Standardized paper
Standardized paper - experimental	Elec_e1hr.exe	Standardized paper
· Query Data
By Citation-Control	Ubd_ui5hr.exe	Find papers by control data
By Citation-Experimental	Ubd_Bi6hr.exe	Find papers by experimental data
By Method	Ubd_ui3hr.exe	Find papers by methods
Universal Biology Database
· Reformat Data
Make Connections
Enter Data Pairs-Control	Dpair_in.exe	Enter control data pairs
Enter Data Pairs-Experimental	Dpair_in_ex.exe	Enter experimental data pairs
View Connections
Data Pair Library	Ubd_ui77hr.exe	View, sort, and filter data pairs
Find Connections
Query Data-Control	Ubd_ui1hr.exe	Find control patterns
Query Data-Experimental	Ubd_ui1ehr.exe	Find experimental patterns
Query Data-CO+EX	Ubd_ui1cehr.exe	Find control and experimental patterns
Digital Libraries
· Change
Steady State Change
Enter Data	Ubd_ch_steadystate.exe	Enter steady state data
Query Data	Query-steadystate.exe	Query steady state data
Transitional Change
Enter Data	Ubd_ch_transitional.exe	Enter transitional data
Query Data	Query-transitional.exe	Query transitional data
· Patterns
Experiments as Equations
Unfolding Complexity	Opticaldensitymol.exe	Simulator for experiments as equations
Engineering	Hippo.exe	Reverse and forward
Blueprint
Enter Data	Conrep.exe	Enter blueprint data
View Data	Conrep_outhr.exe	View blueprint data
Query Data	Ubd_core_out.exe	Query blueprint data
Unintended Consequences
Concentration Trap	Da01_outhr.exe	Explore pitfalls of concentration data
Systems Biology Two
Folders		Development, disease, exposure
Documents
EBS 2009	Ubd_2009.exe	Software package for 2009
Reports	Reports.exe	2001 to present
RuleBook	RuleBook.exe	Guidelines to a mathematical biology
Forms/Templates	Docsforms.exe	Data entry tools
3. Set Up
Install reader	W_adobe_reader	Install Adobe Reader
	AdbeRdr90_en_US.exe	Install reader for Adobe Acrobat 9.0
	Microsoft WSE 3.0 Runtime.msi	May be needed to install - Reader 9.0
	dotnetfx.exe	May be needed to install - WSE 3.0
	WindowsInstaller-KB884016-v2-x86	May be needed to install - dotnetfx
Installation	Readme_install_2009.pdf	Installation directions
Read	Read3.pdf	Introduction / Help
4. Enter Data
Citation	Issb_cit.exe	Enter citation data
Methods	Issb_met.exe	Enter methods data
Control	Issb_co.exe	Enter control data
Experimental	Issb_ex.exe	Enter experimental data
Enter Data Pairs - Co	Dpair_in.exe	Enter control data pairs
Enter Data Pairs - Ex	Dpair_in_ex.exe	Enter experimental data pairs
Enter Steady State Data	Ubd_ch_steadystate.exe	Enter steady state data
Enter Transitional Data	Ubd_ch_transitional.exe	Enter transitional data
Read	Read4.pdf	Introduction / Help
5. View Data
Citation	Ubd_cit_listhr.exe	Find papers by citation et cetera
Stereology Literature Database - Co	Ubd_sldb_c.exe	Catalogue of stereological data - Co
Stereology Literature Database - Ex	Ubd_sldb_e.exe	Catalogue of stereological data - Ex
Standardized paper - control	Elec_c1hr.exe	Standardized paper
Standardized paper - experimental	Elec_e1hr.exe	Standardized paper
Data Pair Library	Ubd_ui77hr.exe	View, sort, and filter data pairs
Blueprint Data	Conrep_outhr.exe	View blueprint data
Engineering	Hippo.exe	Reverse and forward
Read	Read5.pdf	Introduction / Help
6. Query Data
Citation-Control	Ubd_ui5hr.exe	Find papers by control data
Citation-Experimental	Ubd_bi6hr.exe	Find papers by experimental data
Method	Ubd_ui3hr.exe	Find papers by methods
Proportion-Control	Ubd_ui1hr.exe	Find control patterns
Proportion - Experimental	Ubd_ui1ehr.exe	Find experimental patterns
Proportion - Co+Ex	Ubd_ui1cehr.exe	Find control and experimental patterns
Blueprint	Ubd_core_out.exe	Query blueprint data
Steady State	Query-steadystate.exe	Query steady state data
Transitional	Query-transitional.exe	Query transitional data
Read	Read6.pdf	Introduction / Help
Files
Worksheet-Connection phenotype	Cp_worksheet.docx, .doc, .pdf	Data entry worksheet
Worksheet-Hierarchy	Hi_worksheet.docx, .doc, .pdf	Hierarchy for data entry worksheet
Worksheet-Data entry table	Data_worksheet.docx, .doc, .pdf	Summary table for data entry worksheet
Database Name	Database (.db)	Upgrades
Biology Literature Databases	Issb_pc.db; sysbio.db	Stereology Literature, Universal Biology, and Systems Biology Databases
Systems Biology Two Database	Sysbio.db; sysbio.ini	· Software Tree

Credits

Development Platform

Powerbuilder, Sybase Incorporated, Dublin, CA.

Viewer

The runtime reader Acrobat (9.0, 9.3) is made available as a courtesy of Adobe Systems Incorporated, San Jose, CA.

Disclaimer

The author makes no claims of usability, efficacy, or warranty. The SOFTWARE LICENSE AGREEMENT completely defines the licensed use of this software.

Information in this document is provided in connection with this product. No license, express or implied, or otherwise, to any intellectual property rights is granted by this document. The author assumes no liability whatsoever, and disclaims any express or implied warranty relating to use of this product, including liability or warranties relating to fitness for a particular purpose, infringement of any patent, copyright, or other intellectual property right. The software is not intended for use in medical, life saving, or life-sustaining applications.

The author disclaims all warranties and liabilities for the use of this document and the information contained herein, and assumes no responsibility for any errors that may appear in this document or software package, nor does the author make a commitment to update the information contained herein. The author reserves the right to make changes to this document or software at any time, without notice.

NOTICE OF PROPRIETARY RIGHTS

The Enterprise Biology Software and documentation are the property of Robert P. Bolender. Use, examination, reproduction, copying, disassembly, decompilation, transfer to others, in whole or in part, are strictly prohibited except the express prior written consent of Robert P. Bolender.

readme_install_2009.pdf

May 15, 2010

Notes

SYSTEMS BIOLOGY TWO

Files

Worksheet-Connection phenotype

Worksheet-Hierarchy

Worksheet-Data entry table

Development Platform

Viewer