Software version update highlights (Check newest version here)
Feb 11, 2023
Visual Gene Developer 2.1 Build 797 released
- Users can resize most windows.
- The screen configuration
has been improved to suit high DPI monitors.
- Neural networks support large numbers of inputs and outputs.
Feb 22, 2019
Visual Gene Developer 1.9 Build 785 released
- The neural network toolbox is optimized for large-scale training.
- Neural network training error chart implemented.
- The speed of loading and saving neural network pattern files has been increased.
Aug 11, 2016
Visual Gene Developer 1.7 Build 763 released
- Genomic tRNA web database's address has been changed (http://gtrnadb2009.ucsc.edu/)
Thus, we have fixed an issue of accessing the database.
Thanks to Dr. Baruah who reported this issue!
Jan 30, 2014
Visual Gene Developer 1.4 Build 750
*Right click or option-click the link and choose "Save As..." to download this file
- Network computing has been significantly improved.
Now, Visual Gene Developer maintains highly stable connections to clients without sudden disconnection
Nov 8, 2013
Visual Gene Developer 1.3 Build 737b
- Bug fix: Errors in the 'CAI profile v2' were fixed. Dr. Lahm reported this bug.
Dec 7, 2012
Visual Gene Developer 1.3 Build 737
- Bug fix: Runtime error caused by Windows' international language setting (ex. Dutch) has been fixed.
Now enjoy Visual Gene Developer in Dutch Windows OS.
- New module: 'Random codon mutation' written in VBScript has been added
June 30, 2012
Visual Gene Developer 1.3 Build 732 Download zip file version
*Right click or option-click the link and choose "Save As..." to download this file
- Exporting table data: the algorithm has been optimized. Now it is super fast!!!
- Access to tRNA database: Import tRNA tables from Genomic tRNA Database (http://gtrnadb.ucsc.edu/)
calculate tAI (tRNA adaptation inex)
- GenBank Extractor: Batch process function has been added to process multiple files automatically.
'View' button added.
VGD automatically scans *.fna file while setting *.gbk file
- Artificial Neural Network: 'Normalize data' window has been added. Now normalize raw data easily!
- Importing gene lists from clipboard or file: VGD can check and exclude/include improper DNA sequences containing words other than ATGC.
- New functions: 'Get_ReverseCompl_Seq' added (Get reverse complimentary sequence)
- ETC: Potential errors which were caused under certain Windows locales have been removed (Thanks to Jenny J who reported this error)
June 2, 2012
Visual Gene Developer 1.3 Build 707 Download zip file version
*Right click or option-click the link and choose "Save As..." to download this file
- GenBank Extractor updated: now it can handle intron and exon to extract CDS by handling 'complement' and 'join' features
- Directly import Gene List from Clipboard
May 21, 2012
- Hot fix: Error handling routine added to GenBank Extractor
- Import DNA sequences from FASTA file
- Extract field information from GenBank file
* The current GenBank Extractor doesn't handle introns to extract CDS. Use it for procaryotes. A next version will provide a complete set of functions.
- Calculate tAI (tRNA adaptation index)
- Option for Batch mode added for easy use!!
- In Neural network toolbox, analysis of regression coefficient can be conducted
- ETC
File Processing function add (Menu>Function>File Processing)
In Module Library window, source code is shown in formatted color.
Network computing module has been revised.
April 6th, 2012
Visual Gene Developer 1.2 Build 651
- Version has been updated to 1.2
- The software supports approximate sequence search!!
March 23rd, 2012
Visual Gene Developer 1.1 Build 646 released
- Three new functions were added
o Menu>Function>Parsing>Remove non-alphabetic characters,
o Menu>Function>Reverse complementary seqeunce
o Menu>Function>Degenerate gene sequence
- The software allows to generate degenerate sequences with lots of combination.
- 'Continue training' button was added on the 'Neural Network Configuration' window
Oct 24th, 2011
Visual Gene Developer 1.0 Build 635
- As shown in the below image, Visual Gene Developer didn't run in some non-English Windows operating systems such as French and Spanish. We fixed this problem.
- A computer may have multiple IP addresses that serve as host IP address of a network computing server. Now, Visual Gene Developer automatically scans all available IP addresses and allows a user to choose one of them.
Sept 18th, 2011
Visual Gene Developer 1.0 Build 631
- New function added in the 'mRNA structure view' window.
August 31th, 2011
Visual Gene Developer 1.0 Build 630
- New function: 5 different formatting methods newly implemented
August 28th, 2011
Visual Gene Developer 1.0 Build 627
- Update notice function added.
Visual Gene Developer checks if new version of the software is available.
- 'Save As' showed long file name. We fixed it.
August 23th, 2011
Visual Gene Developer 1.0 Build 622
- Importing data from clipboard generated error. We fixed it.
- 3 profiling modules (GC content, mRNA, CAI) slightly revised to show legend.
August 20th, 2011
Visual Gene Developer 1.0 Build 621
- Minor bug fixed
- Automated software installation provided
July 16th, 2011
Visual Gene Developer 1.0 Build 619
- Web site link modified
- PropertyBag Editor interface improved
- NotePad function added
- Entire source code optimized
July 8th, 2011
Visual Gene Developer 1.0 Build 615
- Basically no changes except downgrading .Net Framework from version 4.0 to 3.5
June 29th, 2011
Visual Gene Developer 1.0 Build 614
- Windows interface updated including back-translation, CAI&GC content analysis
- Sample file added: 'Sample 2DColorMap - Trained network.vgn'
June 11th, 2011
Visual Gene Developer 1.0 Build 611
- Network computing module improved. Data transfer speed increased up to 5 times!!
- 'Draw' function added on the 'mRNA optimization'. Now it's easy to compare mRNA profiles between before and after optimization.
- Sample user-defined module added: Check '2D Color map using ANN' in the 'Module Library' window
April 27th, 2011
Visual Gene Developer 1.0 Build 609
- A few bugs fixed
- Now, 64 Bit Windows OS is supported!!
March 12th, 2011
Visual Gene Developer 1.0 Build 606
- Bugs fixed
- New function added: GeneService.Get_CodonUsage_RSCU
- New user-defined function added: 'Codon bias diagram'
Check for Usage & Source code
February 27th, 2011
Visual Gene Developer 1.0 Build 602
- Software development platform upgraded from Visual Studio .Net 2008 to Visual Studio .Net 2010
February 10th, 2011
Visual Gene Developer 1.0 Build 600
- New class 'CustomUI' developed for graphics Check details
- 3 user-defined modules updated to version 2: GC content profile v2, mRNA profile v2, CAI profile v2
- Network/multi-threaded computing module upgraded for optimized performance
December 17th, 2010
Visual Gene Developer 1.0 Build 597
- 3 bugs fixed: 'Paste' function in the Neural network windows
Opening new codon usage table
'Zoom' function in pop-up menu in the mRNA viewer
October 30th, 2010
Visual Gene Developer 1.0 Build 594
- We renamed the software from 'Visual Gene Designer' to 'Visual Gene Developer'
- Our software website has been greatly renewed.
- mRNA optimization functions (Specialized widow and Class functions) were implemented into the software.
October 18th, 2010
Visual Gene Developer 1.0 Build 571 The software has been greatly improved!!!
- Main menu: Short keys were added
- Preference window: A user can set cache folder and total number of caches for mRNA structure prediction
- Gene construct designer window:
To assign Gene element type, multiple cloning site and restriction enzyme site can be used
'Delete all gene constructs except current one' function was added in the 'Edit' menu
''Translate restriction enzyme' function was added in the ''Function' menu
- Configuration of gene optimization window: Caption is now available and overall performance is improved
- Gene optimization window: Sorting function is added. Process monitoring Property Bag was improved
- Module Editor window
Line number is shown in the window and cursor will be moved to the point where error occurs
'Hide/Show Property Bag' function was added to give more space to a user to edit source code
- Default project, Script, Property Bag, w-table and sample files were modified or newly included
- 3 'Manipulation' modules written in VBScript were added:
'Silent removal v2'
'Silent removal of potential polyadenylation sites'
'Silent removal of potential intron cryptic splice sites'
October 14th, 2010
Visual Gene Developer 1.0 Build 567
- Update problem of 'W-table file' selection list drop box on 'Codon optimization' window fixed.
- New module added: GeneService.Current_WTableFile
- User-defined function added: 'CAI profile diagram' on a toolbox
Paste any sequence to 'Workspace' window and then double click on 'CAI profile diagram' in Toolbox window. When analysis is done, paste clipboard data to Excel or other software to draw a plot.
October 10th, 2010
Visual Gene Developer 1.0 Build 565
- 'mRNA structure viewer' window: clear text for sequence number used. Copy function added.
Now, Visual Gene Developer supports copy & paste function as shown in the below figure (Excel).
October 8th, 2010
Visual Gene Developer 1.0 Build 564
- 3 minor bugs fixed
- 1 sample Project file "Sample construct - GFP.vgp" included
- 5 sample gene construct files included
- 1 sample user defined function "Sample Random sequence" added: it generates 1000 random sequences
September 3rd, 2010
Visual Gene Developer 1.0 Beta (Build 562)
- New features: Zoom and syntax coloring in the 'Module Editor' window
- New collection of defined sequences added for 'Search sequences' and 'Silent removal of sequences' window
July 28th, 2010
Visual Gene Developer 1.0 Beta (Build 560)
- New Window added: 'Codon optimization' window added (Menu: Function > Codon optimization)
- New function added: new functions were added to 'Workspace' window
- Nc: internal algorithm modified
July 23th, 2010
Visual Gene Developer 1.0 Beta (Build 555)
- New function added: Silent Removals Window added (Menu: Function > Silent removal of sequences)
- Bug fixed: Silent_Removal functions had known bugs and were fixed now.
- Redesigned: Sequence comparison window was reorganized.
July 20th, 2010
Visual Gene Developer 1.0 Beta (Build 551)
- New function: Search Sequence window (Menu: Analysis > Search Sequences)
- Gene Analysis: Number of effective codons, Nc (Menu: Analysis > CAI, GC content and Nc)
- Class 'GeneService': the above functions were included for script programming
Function Calculate_Nc (Source_Seq As String, Calculate_CodonUsage As Boolean) As Single
Function Get_SearchSequences_Str(Source_Seq As String, FindWhat_Seq As String) As String
July 5th, 2010
Visual Gene Developer 1.0 Beta (Build 549)
- Artificial neural network model: Network map analysis tool was added.
Just double-click on a diagram in the 'Neural Network Configuration' window.
The 'Neural Network Map Analysis' window shows weight factors and threshold values of networks as color and width.
- New user defined function: mRNA local Gibbs free energy diagram
The predefined function analyzes mRNA secondary structures of all partial sequences of a test gene and then exports average Gibbs free energy to clipboard. Using drawing software such as SigmaPlot, a user can draw the following diagram.
- PropertyBag: maximum number of properties was increased to 35.
June 27th, 2010
Visual Gene Developer 1.0 Beta (Build 545)
- Artificial neural network model: Pattern analysis function was added
Example: Ternary plot to test 3 input variables
- Manual search, Automated search: strange behavior of start and stop button fixed
- File save: saving unnecessary information due to program bug was removed
- Project window: no-updating problem fixed
May 7th, 2010
Visual Gene Developer 1.0 Beta (Build 540)
- Neglecting file save function of neural network file was corrected
- AppService.InstantMsg module was improved.
- Supports maximum 5 multiple instances of NeuralNet class including 'NeuralNet', 'NeuralNet2', 'NeuralNet3', 'NeuralNet4', and 'NeuralNet5'.
- New modules were added to mRNApredict: Get_AvgEnergy, Get_SumEnergy, Get_AvgProbability, Get_SumProbability
- New predefined module, Check stable mRNA structure, was added
April 30th, 2010
Visual Gene Developer 1.0 Beta (Build 538)
- Real time back translation of DNA sequences when you import Gene Construct List file
- Number of mRNA structure caches is 5,000
