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Release Notes for

ENTERPRISE BIOLOGY SOFTWARE 2011 (Version 11.0)

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Description of the Software

The Enterprise Biology Software (EBS 2011; Version 11.0) includes:

· Mathematical Mapping

· Information Infrastructure

· Database Upgrades (2011)

· Stereology Literature Database

· Universal Biology Database

· Systems Biology Database

· Digital Library Database

Before you begin, you need:

Software	Enterprise Biology Software 2011; 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 11.0; 600+ 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

Programs and relational databases are installed in a client/server configuration. The software uses a runtime database engine (rtdsk50.exe) that connects user interfaces to a backend server. During 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 Enterprise Biology Software Package (2011) from the DVD

· Step 1: Put the EBS 2011 DVD in the center ring (80 mm) of the DVD drive, close the door, and the installation starts automatically. Run the installation program. NOTE: When installing the software on a computer running Windows 7 Professional, two program directories (Program Files and Program Files (X86)) may exist. In such a case, open the folder on the DVD marked Windows 7-32-64 and double click on setup.exe to launch the installation.

· Step 2: Install Adobe Acrobat Reader 9.0. Click on the title screen and then select SET UP. Click on install reader and then click on the RUN button. Directions will appear.

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 related to the resolution, color (High Color or True Color), or font size (Small).

· The current resolution setting (1280 by 1024 pixels) may exceed that of your monitor and/or graphics card, obscuring parts of the screen. If so, use on scroll buttons (when 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 Enterprise Biology Software

Press the Start button on the toolbar; select All Programs, EBS 2011, and Uninstall EBS 2011. This is the recommended procedure. Alternatively, the programs can be removed from the control panel.

Running the Enterprise Biology Software

Starting the Software

To start the program, double click the EBS 2011 icon.

Selecting programs

In the opening screen, select an item in the menu. Note that the most recent release of Adobe Reader (i.e., 9.0) must be installed to view the PDF text files. The EBS software uses a hardcoded path for PDF files: C:\Program Files\Adobe\Acrobat 9.0\Acrobat.exe. Note that both versions 10 and 11 use Acrobat 9.0.

Technical Issues

Program notes

· The default paper size for printing is 8.5 x 14 inches (Legal).

· A sort button can have two functions (left mouse click = ascending; right mouse click = descending.

· Some of the programs begin by loading large database files and may take several minutes - depending on the memory, processor, 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 setting the screen resolution.

· The new screen resolution (1280 by 1024 pixels) may cause a problem on older computers and on some laptops. If the screen becomes partially obscured click on the scroll button (if present).

· Installing the new software (2011) changes the ODBC setting for the database. This may interfere with earlier EBS programs running on the same computer.

· 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).

ENTERPRISE BIOLOGY SOFTWARE (11.0) 2011

Window Name (as it appears in on the screen)	Program (.exe) or File (.pdf)	Notes
MATHEMATICAL MAPPING	UBD_2011.exe	Enterprise Biology Software 2011
1. Documents		Progress reports
2011	Paper12.pdf	Progress report for 2011
2010	Paper11.pdf	Progress report for 2010
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	DocsForms.exe	Data entry forms and templates
Read	1documents2011.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
Change Units	Change_units.exe	Convert data units
· 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
View Data	Query-transitional.exe	Query 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		Implications of biological complexity
Concentration Trap	Da01_outhr.exe	Explore pitfalls of concentration data
Systems Biology Two		A quantitative approach
Triplets		Parts by three
Find Data (Valences)	Ubd_valences.exe	Identify valences of triplets
Enter Data	Triplet.exe	Enter triplet data from UBD
View Data	Triplet_view.exe	View triplets
Query Data	Triplet_query.exe	Query triplets
Organism Codes		Rules of organization
Enter Data	Ubd_org_code.exe	Enter organism codes
View Data	Ubd_code_view.exe	View organism codes
Query Data	Ubd_code_query.exe	Query organism codes
Query2 Data	Ubd_code_query2.exe	Query organism codes
Enter Data – Phenotype Equations	Ubd_eq_ph.exe	Enter phenotype equations
View Data – Phenotype Equations	Ubd_eq_ph_view.exe	View phenotype equations
Read	2softtree2011.pdf	Introduction / Help
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_2011.pdf	Installation directions
Read	3setup2011.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
Data Pairs - Co	Dpair_in.exe	Enter control data pairs
Data Pairs - Ex	Dpair_in_ex.exe	Enter experimental data pairs
Steady State Data	Ubd_ch_steadystate.exe	Enter steady state data
Transitional Data	Ubd_ch_transitional.exe	Enter transitional data
Triplet Data (find)	Ubd_valences.exe	Identify valences of triplets
Triplet Data	Triplet.exe	Enter triplet data from UBD
Organism Codes	Ubd_org_code.exe	Enter organism codes
Phenotype Equations	Ubd_eq_ph.exe	Enter phenotype equations
Read	4enterdata2011.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
Triplets	Triplets_view.exe	View triplets
Organism Codes	Ubd_code_view.exe	View organism codes
Phenotype Equations	Ubd_eq_ph_view.exe	View phenotype equations
Read	5viewdata2011.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
Triplets	Triplets_query.exe	Query triplets
Organism Code 1	Ubd_code_query.exe	Query organism codes
Organism Code 2	Ubd_code_query2.exe	Query organism codes
Read	6querydata2011.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; issb_pc.ini	· Stereology Literature & Universal Biology Databases
Systems Biology Two Database	Sysbio.db; sysbio.ini	· Software Tree
Digital Library Database	EBS_Lib.db; dig_lib.ini	· New

Credits

Development Platform

· Powerbuilder, Sybase Incorporated, Dublin, CA.

Viewer

· The runtime reader Acrobat (9.0) 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, nor does the author make a commitment to update the information contained herein. The author reserves the right to make changes to this document 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_2011.pdf

December 15, 2011

Notes

MATHEMATICAL MAPPING

Files

Worksheet-Connection phenotype

Worksheet-Hierarchy

Worksheet-Data entry table

Viewer