Release Notes for

 

ENTERPRISE BIOLOGY SOFTWARE 2015 (Version 15.0)

© Copyright 2001 - 2015 Robert P. Bolender and Licensors

All rights reserved.

******************************************************************

 Description of the Software

The Enterprise Biology Software (EBS 2015; Version 15.0) includes:

·        Information Infrastructure

·        Database Upgrades (2015)

·     Stereology Literature Database

·     Digital Library Databases

·     MRI Databases

                      

Before you begin, you need:

Software   Enterprise Biology Software 2015 – DISORDER - ORDER
DVD Drive   To install the program
Processor  Recent Intel or AMD personal computer
RAM 4+ GB of memory (recommended)
Disk space  EBS Software Package 15.0: ~4 GB of hard disk space on the C drive
OS Microsoft Windows 7, 8, OR 10 - preferably
Resolution  1280 by 1024 pixels (right click desktop Properties/Settings) with exceptions
Display Properties Appearance tab - set Scheme to Windows Standard
Color Depth High Color or True Color (recommended)
Font Size  Small

               

 

Installation Overview

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. 

In windows 7, 8, and 10, Microsoft defines two Program Files, one for 32 bit (C:\Program Files (x86) and the other for 64 bit (C:\Program Files).  Formerly, the 32 bit OS used C:\Program Files.  To accommodate the large sizes of the new diagnosis databases, only the installation program for Windows 7, 8, and 10 is included in software package.

 

Installation

Install the Enterprise Biology Software Package (2015) from the DVD

    ·        Step 1: Uninstall previous versions of the Enterprise Biology Software.

·        Step 2: (Windows 7 - 10) - Put the EBS 2015 DVD in the center ring (80 mm) of the DVD drive, close the door, and the installation starts automatically.  Run the installation program.  If instructed to run the program as administrator, highlight the Setup.exe program on the DVD, right click, and select <Run as administrator>. 

·        Step 2: Install Adobe Acrobat Reader 11.0.  When the installation is completed, double click on the EBS 2015 icon.  Click on the title screen and then select SET UP.  Click on install reader and then 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 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, obscuring parts of the screen.  If so, use on scroll buttons (when present).

·        It is always a good idea during an installation to have no open applications and no applications running in the background (this may include anti-virus software, crash monitoring software, and system diagnostic software).

  

Uninstall the Enterprise Biology Software Package

Press the Start button on the toolbar; select All Programs, EBS 2015, and Uninstall EBS 2015.  This is the recommended procedure.  Alternatively, the software 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 2015 icon or start it from the program list - Start/programs/EBS 2015.

Selecting programs

In the opening screen, select an item in the menu.  Note that the most recent release of Adobe Reader (i.e., 12.0) must be installed to view the PDF text files.  The EBS software uses a hardcoded path for PDF files: C:\Program Files (x86)\Adobe\Reader 12.0\Reader\AcroRd32.exe.

  

Technical Issues

Program notes

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

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

·        Some of the programs begin by loading large database files that 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 following the directions given above (See: Before you begin…).

·        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).    

·        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). 

·        When the software is installed on computers with solid state drives (SSD), the contents of the standardized papers screen do not display.  No fix can be suggested.

 

ENTERPRISE BIOLOGY SOFTWARE (15.0) 2015/16 

Window Name (as it appears in on the screen)

Program (.exe) or File (.pdf)

Notes

BIG DATA

UBD_2015.exe

Enterprise Biology Software 2015/2015

1. Documents

 

Progress reports

    2015

Paper16.pdf

Progress report for 2015

    2014

Paper15.pdf

Progress report for 2014

    2013

Paper14.pdf

Progress report for 2013

    2012

Paper13.pdf

Progress report for 2012

    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

1documents2015.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

    Enter Data Pairs-All CO Levels

Dpair_in_total.exe

Enter control data pairs

    Enter Data Pairs-All EX Levels

Dpair_in_total_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

2softtree2015.pdf

Introduction / Help

3. Set Up

 

 

    Install reader

W_adobe_reader

Install Adobe Reader

 

AdbeRdr90_en_US.exe

Install reader for Adobe Acrobat 11.0

 

Microsoft WSE 3.0 Runtime.msi

May be needed to install - Reader 11.0

 

dotnetfx.exe

May be needed to install - WSE 3.0

 

WindowsInstaller-KB884016-v2-x86

May be needed to install - dotnetfx

    Installation

Readme_install_2015.pdf

Installation directions

    Read

3setup2015.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

4enterdata2015.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

    Stereology Literature Database - Co

Stereology_cc_view.exe

Table of stereological data - Co

    Stereology Literature Database - Ex

Stereology_ex_view.exe

Table 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

    MRI Diagnosis

Mri_diagnosis_view.exe

View diagnosis mathematical markers

    MRI Normal

Mri_noraml_view.exe

View normal mathematical markers

    MRI Disease

Mri_disease_view.exe

View disease mathematical markers

    MRI normal+Disease

Mri_nor_dis_view.exe

View nor+dis mathematical markers

    MMarker X:Y

Datapair_view.exe

View data pair mathematical markers

    MMarker X:Y:Z

Triplet_marker_view.exe

View triplet mathematical markers

    MMarker All In

All_in_view.exe

View all mathematical markers

    MRI Q Diagnosis 100%

Mri_q_diag_100.exe

View unique quadruplet markers

    MRI T Diagnosis 100%

Mri_t_diag_100.exe

View unique triplet markers

    MRI T Small

Mri_t_small.exe

View total triplet markers (truncated)

    MRI T Big

Mri_t_big.exe

View total triplet markers (complete)

    Read

5viewdata2015.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

    Stereology Literature Database - Co

Stereology_cc_query.exe

Table of stereological data - Co

    Stereology Literature Database - Ex

Stereology_ex_query.exe

Table of stereological data - Ex

    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

    MRI Diagnosis

Mri_diagnosis_query.exe

Query diagnosis mathematical markers

    MRI Normal

Mri_noraml_query.exe

Query normal mathematical markers

    MRI Disease

Mri_disease_query.exe

Query disease mathematical markers

    MRI normal+Disease

Mri_nor_dis_query.exe

Query nor+dis mathematical markers

    MMarker X:Y

Datapair_query.exe

Query data pair mathematical markers

    MMarker X:Y:Z

Triplet_marker_query.exe

Query triplet mathematical markers

    MMarker All In

All_in_query.exe

Query all mathematical markers

    MRI Triplet Big - Query

Mri_t_big_query

Query control and experimental markers

    Read

6querydata2015.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

    Template-Markers for quadruplets

Template_quadruplet.xlsx

Converts data to mathematical markers

    Template-Markers for triplets

Template_triplet.xlsx

Converts data to mathematical markers

Database Name

Database (.db)

Upgrades

    Biology Literature Databases

Issb_pc.db; issb_pc.ini

·    Stereology Literature & Universal Biology Databases

    Digital Library Database

EBS_Lib.db; dig_lib.ini

·    New in 2010

    MRI Database

MRI_DB; mir_db.ini

·    New in 2012

    MRI_2014 Database

MRI_2014; mri_2014.ini

·    New in 2014

    MRI-Q-DIAG-100

Access Database File (.accdb)

·    New in 2014

    MRI-T-DIAG-100

Access Database File (.accdb)

·    New in 2014

    MRI-T-SMALL

Access Database File (.accdb)

·    New in 2014

    MRI-T-BIG

Access Database File (.accdb)

·    New in 2014

   MRI_T_DUPS_2015

Access Database File (.accdb)

·    New in 2015

    MRI_MARKERS_PLOT

Access Database File (.accdb)

·    New in 2015

 

Credits 

Development Platform

·        PowerBuilder, Sybase Incorporated, Dublin, CA. 

·        Excel and Access (64 bit), Microsoft, Redmond, WA

Viewer

·        The runtime reader Acrobat (11.0) 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. 

© Copyright 1994-1997 Robert P. Bolender and the University of Washington 

© Copyright 2001-2015 Robert P. Bolender and Licensors 

All rights reserved. 

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_2015.pdf

December 15, 2015