Tool: New Mac program for molecular biologists
6
gravatar for vytarasov
14 months ago by
vytarasov110
Germany
vytarasov110 wrote:

I would like to present here a program - BioLabDonkey - for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac - Swift. The program can be downloaded from mac App Store - https://apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12 It is not free but it is definitely affordable for students. It is one time purchase app, no subscription. New features will be added regularly. The program has a following list of features:

  • Opens files (for DNA, protein, alignment) with the extensions: .txt, .rtf, .fasta, .fas, .fa, .fsa, .ffn, .fna, .seq, .ape, .gb, .gbk, .ab1, .bldna, .fas, .faa, .seq, .gp, .blprotein, .pdb, .fastq, .aln, .blalignment, .jpg, .tiff, .png,
  • Saves files (for DNA, protein, alignment) with the extensions: .txt, .rtf, .fasta .fas, .fa, .fsa, .ffn, .fna, .seq, .gb, .gbk, .ab1, .bldna, .fas, .faa, .seq, .gp, .blprotein, .blalignment, .pdf, .eps, jpg, png
  • Transcribe, reverse complement and translate DNA sequence
  • Find open reading frames (ORFs),
  • Find sequence motifs (repeats, palindromes, stem loops and arbitrary sequences) in DNA sequence,
  • Generate primers,
  • View ABI sequencing chromatogram, edit sequence,
  • Generate ORF silent mutations,
  • View GC content, CpG islands and Stem Loops,
  • Generate Plasmid, Linear map,
  • Generate and edit DNA, protein features for genbank, genpept format files,
  • Generate features database and perform automatic features annotation,
  • Copy/paste the selected DNA sequence with features,
  • Find DNA restriction sites and DNA fragments,
  • Genome viewer,
  • Virtual DNA gel,
  • Multiple alignment and realignment of DNA and protein sequences,
  • Phylogenetic tree,
  • 3D Protein/DNA/RNA viewer,
  • Prediction of protein secondary structures,
  • Hydropathicity/pI plots,
  • Limited proteolysis,
  • Find protease sites and protein fragments,
  • RNA-Seq DE - Genes and miRNAs differential expression,
  • Calculator for - Dilution, Molarity, Ligation, SDS PAG, Ammonium sulfate, Bacteria growth Nucleic acid OD conversion,
  • Units conversion for DNA and protein,
  • Colonies/Cells/Spots counting,
  • Analysis of Gel/Blot photo and calculation of relative fold-change in selected Gel/Blot bands/spots,

The site with BioLabDonkey Help Book is here - https://molbiolinfo.home.blog

Any question/advice is welcome!

tool software • 2.0k views
ADD COMMENTlink modified 5 weeks ago • written 14 months ago by vytarasov110
0
gravatar for vytarasov
10 months ago by
vytarasov110
Germany
vytarasov110 wrote:

The BioLabDonkey update - 1.3 - is released in Mac App Store with
- Bug fixes,

ADD COMMENTlink modified 9 months ago • written 10 months ago by vytarasov110
0
gravatar for vytarasov
7 months ago by
vytarasov110
Germany
vytarasov110 wrote:

The BioLabDonkey Version 1.4 is released with:
- Added a new feature to generate and use the custom list of miRNAs for miRNA-Seq differential expression analysis.
- Fixed a bug causing incorrect locations of genbank features after some insertion/deletion in DNA sequence.

ADD COMMENTlink written 7 months ago by vytarasov110
0
gravatar for vytarasov
6 months ago by
vytarasov110
Germany
vytarasov110 wrote:

The BioLabDonkey Version 1.6 is released with:
- Improved performance in Protein Tab (the secondary structure prediction speed up).
- Bug fixes .

ADD COMMENTlink modified 6 months ago • written 6 months ago by vytarasov110
0
gravatar for vytarasov
5 months ago by
vytarasov110
Germany
vytarasov110 wrote:

I was asked to add to BioLabDonkey an option to read xdna files from Serial Cloner app. It looks right now, at academic institutions, there is a demand for a mandatory Catalina upgrade, to 64bit, and Serial Cloner is not compatible with this macOS. So I have made parser for xdna files and have made the following BioLabDonkey update :

BioLabDonkey Version 1.8 :
- App opens .xdna files created by Serial Cloner and DNA Strider programs,
- Added an option to generate a primers list in Primers window. The list can be imported/exported as .txt,
- Bug fixes

ADD COMMENTlink modified 5 months ago • written 5 months ago by vytarasov110
0
gravatar for vytarasov
5 months ago by
vytarasov110
Germany
vytarasov110 wrote:

The BioLabDonkey Version 1.9 is released with:
* App opens .dna files created by SnapGene program.
* Added an option to remove the plasmid name from Plasmid Map.
* Bug fixes.

ADD COMMENTlink written 5 months ago by vytarasov110
0
gravatar for vytarasov
4 months ago by
vytarasov110
Germany
vytarasov110 wrote:

Dear users, if there is a need for a new feature implemented in the program let me know here !

ADD COMMENTlink written 4 months ago by vytarasov110
0
gravatar for vytarasov
3 months ago by
vytarasov110
Germany
vytarasov110 wrote:

The BioLabDonkey Version 1.10 is released.

  • For a new GenBank feature the feature qualifier is sized and positioned automatically to meet the GenBank format requirements.
  • Bug fixes and minor interface improvements.

In a coming next version a new feature - assembly of reads from .ab1 (or .txt) files - will be added. This function is designed for not high number of reads and it is independent of read size.

ADD COMMENTlink written 3 months ago by vytarasov110
0
gravatar for vytarasov
9 weeks ago by
vytarasov110
Germany
vytarasov110 wrote:

The BioLabDonkey Version 2.0 is released.

  • New feature - Assembly of DNA sequencing reads from .ab1 or .txt files for the amount of files up to several hundreds.
  • New feature - Text Map of DNA sequence with marked genbank features, translation frames and restriction site positions. 
  • In Alignment Tab DNA sequence can be exchanged to the reverse-complement one.
  • Bug fixes.
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by vytarasov110
0
gravatar for ofbaltaci
5 weeks ago by
ofbaltaci0
ofbaltaci0 wrote:

Hi, I was wondering if it's possible to get a trial run or a detailed tutorial video so that I can understand if it's worth purchasing for my needs. I have used Serial Cloner for a long time and was quite happy with it until getting a new Mac... I don't want to use Snapgene so seriously considering buying this if it works fine. I'll also purchase for my group (10 members) but it all comes down to whether the app is what we need. Looking forward to hearing from you! Oz

ADD COMMENTlink written 5 weeks ago by ofbaltaci0
0
gravatar for vytarasov
5 weeks ago by
vytarasov110
Germany
vytarasov110 wrote:

Hi Oz, At Apple App Store there is no such a functionality as trial version. All tutorial materials (some small updates are missing) you can find at this website -

https://molbiolinfo.home.blog/biolabdonkey-features/

What is not there is a description for assembly function, this function is new and I will add the description soon. There is also one video, without sound, for the restriction analysis in BioLabDonkey. I plan to add more tutorial videos, for other functions.

Several month ago I have been asked by one head of the lab in University of Arizona a similar question about usage of BioLabDonkey instead of Serial Cloner. For his needs I have made parser for Serial Cloner xdna files and added several new features. You can ask him about his experience with BioLabDonkey. His webpage info - https://medicine.arizona.edu/person/michael-s-kuhns

And, if you would like to have some new features or improvements in BioLabDonkey I am always open to make them.

Best,
Valeriy

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by vytarasov110
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