Tool: New Mac program for molecular biologists
6
gravatar for vytarasov
11 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 • 1.3k views
ADD COMMENTlink modified 18 days ago • written 11 months ago by vytarasov110
0
gravatar for vytarasov
7 months ago by
vytarasov110
Germany
vytarasov110 wrote:

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

ADD COMMENTlink modified 6 months ago • written 7 months ago by vytarasov110
0
gravatar for vytarasov
4 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 4 months ago by vytarasov110
0
gravatar for vytarasov
12 weeks 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 12 weeks ago • written 12 weeks ago by vytarasov110
0
gravatar for vytarasov
9 weeks 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 9 weeks ago • written 9 weeks ago by vytarasov110
0
gravatar for vytarasov
7 weeks 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 7 weeks ago by vytarasov110
0
gravatar for vytarasov
18 days 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 18 days ago by vytarasov110
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