| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| README.txt | 2012-09-23 | 5.1 kB | |
| BioWord.zip | 2012-09-23 | 1.6 MB | |
| BioWordTutorial.doc | 2012-04-01 | 646.1 kB | |
| BioWord Developer_s Manual.pdf | 2012-03-29 | 474.8 kB | |
| BioWord User Manual.pdf | 2012-03-29 | 895.9 kB | |
| BioWord.dotm | 2012-03-21 | 1.9 MB | |
| Biobar Developer_s Manual V3.pdf | 2012-01-02 | 465.5 kB | |
| BioBar User Manual V3.pdf | 2012-01-02 | 871.7 kB | |
| BioBar V3.dotm | 2012-01-02 | 1.7 MB | |
| Biobar V2.01.dotm | 2011-07-27 | 1.3 MB | |
| Biobar User Manual V2.01.pdf | 2011-07-27 | 488.1 kB | |
| Biobar Developer_s Manual V2.01.pdf | 2011-07-27 | 466.6 kB | |
| BioBarTest.doc | 2011-07-23 | 48.6 kB | |
| Biobar Developer_s Manual V2.pdf | 2011-07-17 | 468.9 kB | |
| Biobar User Manual V2.pdf | 2011-07-17 | 486.0 kB | |
| Biobar V2.dotm | 2011-07-17 | 1.3 MB | |
| BIOBAR_DEVELOPERS_MANUAL.pdf | 2011-07-15 | 130.0 kB | |
| BioBar_User_Manual.pdf | 2011-07-15 | 463.0 kB | |
| Biobar.dotm | 2011-07-15 | 798.7 kB | |
| Totals: 19 Items | 14.5 MB | 5 |
BioWord README ------------------------ Description ------------------------ BioWord is a powerful biological sequence editor operating in the most convenient of places: inside your usual word-processor (Microsoft Word 2007 and 2010). Easy to install and embedded into a Microsoft Office Ribbon, BioBar allows instant access to most sequence manipulation and editing needs, such as reverse-complementing, translating or FASTA formatting, and features a full suite of sequence search methods, pair-wise alignment and motif discovery. ------------------------ Contact ------------------------ E-mail lanzald1@umbc.edu or erill@umbc.edu with bugs/questions/comments. Alternate download site: http://compbio.umbc.edu/3655/ ------------------------ Requirements ------------------------ (Windows) Microsoft Word 2007+ ------------------------ Installation and Use ------------------------ For installation instructions and detailed explanations of functionality and usage, see the User's Manual PDF This program is distributed under GNU General Public License; please cite accordingly. ------------------------ Extension Ideas ------------------------ -Extend to Mac Office ---->(pre-2010)-translate VBA to Applescript ---->(2010+)-create equivalent of Ribbon/UI -Test portability to OpenOffice (Feel free to contribute to this list by e-mailing lanzald1@umbc.edu or erill@umbc.edu) ------------------------ Version History ------------------------ BioWord uploaded 9.23.2012 -Fixed bug with character recognition BioWord uploaded 6.13.2012 -Fixed bug with translation map BioWord Uploaded 4.02.2012 -Fixed LaPlace pseudocount calculations -Fixed bug with consensus logo printing (logo sizes are more consistent) BioWord Uploaded 3.31.2012 -Added mouseover text to Userforms -Added support for FASTA sequences in the format >header@sequence -Fixed bug with Gibbs/Greedy IC calculations -Fixed bug with Substring Search when using IUB BioWord Uploaded 3.28.2012 -Expanded parameter information in Gibbs/Greedy results -Expanded parameter information in alignments -Added cancel button to lengthy operations (i.e. Search, Substrings, Window GC, etc) -Fixed problem with masking in Gibbs/Greedy Sampling, allows user to mask positions to the left and right of the sequence BioWord Uploaded 3.21.2012 (Unavailable) -Name change -Updated User manual -Allows multiple motif results for Greedy/Gibbs sampling via masking -Added Progress Bar with cancel option for Greedy/Gibbs and Dyad Motif (fixes locking up problem) -Different color highlights to differentiate Gibbs/Greedy Sampling -Includes IC content for motif in Gibbs/Greedy Sampling -Allows table input (i.e. making a consensus logo from Greedy/Gibbs Sampling motif results) -Results will be printed outside of a table if the cursor is inadvertently inside one -added "reverse complement"/"reverse" to a resultant sequence header after each respective operation -alignment output in Raw/GenBank mirrors BLAST/CLUSTALW output -added PAM250, PAM120, BLOSUM50, and GONNET score matrices for protein sequences -Includes frame for ORFs -Optionally searches reverse complement sequence for ORFs (differential highlighting) -More detailed screentips for Ribbon buttons -Added Jaspar matrix format for PSFM output for the Consensus Logo -Added an epsilon value to determine whether two bases are similarly frequent when generating a consensus logo -Added option to have window %GC results plotted in a Microsoft graph BioBar V3 Uploaded 1.1.2012 -Fixed some problems with options -Added options for protein genomic frequencies -Updated User Manual -Fixed scaling with Consensus Logo Biobar V3 Uploaded 11.27.2011 -Reworked the class structure to allow for future customization (introduced ScoreMatrix class and removed Matcher module) -PSFM prints with Consensus Logo Biobar V2.01 Uploaded: 07.23.2011 -Added EventHandler so that there is no prompt to save BioBar.dotm when Word is closed -Added customizable reference bar to Consensus Logo -Perfected use of IUB codons in searches/motif discovery -Implemented constants of sequence types and output locations/modes -Cosmetic changes in printing tables from search results ------------------------ BioBar V2 Uploaded: 07.17.2011 -Substring/Gapped Search, Dyad Pattern/Motif Discovery, Gibbs/Greedy Sampling, and Consensus Logo can now be used with protein sequences -Centralized protein scoring options in the Advanced Options pop-up and made it more intuitive to add new protein scoring matrices -Added new Score Thresold to Substring/Gapped Search and Dyad Motif Discovery -Decreased font size in codon-usage table prompt to avoid word-wrapping -Fixed numerous bugs, including: ----> GenBank line overlap ----> Multiple/unnecessary error messages ----> NGram displaying fragments at the end of a sequence ----> MW calculation error ----> Highlight sub ----> Display of sequence names in tables ----> Subscript Out of Bounds error (Gibbs/Greedy Sampling)