Tool:BioLabDonkey - new Mac program for molecular biologists

Question

[vytarasov]

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!

[vytarasov]

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

• Bug fixes,

[vytarasov]

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.

[vytarasov]

The BioLabDonkey Version 1.6 is released with:

• Improved performance in Protein Tab (the secondary structure prediction speed up).
• Bug fixes .

[vytarasov]

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

[vytarasov]

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.

[vytarasov]

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

[vytarasov]

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.

[vytarasov]

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.

[ofbaltaci]

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

[vytarasov]

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

[vytarasov]

The BioLabDonkey Version 2.5 .

New feature - easy cloning of restricted DNA fragments with GenBank features in three clicks. In DNA1 (DNA2) Tab, select the restriction sites in the table, select the restricted fragment in the table and press the “DNA2” (“DNA1”) button to clone the fragment into the DNA sequence in DNA2 (DNA1) Tab.

New feature - a table with amino acid composition. Amino acids can be marked/unmarked in different colours.

There are options to choose the translation frames to display in the Text Map and to copy/paste a reverse strand of the selected DNA sequence with features.

[vytarasov]

The BioLabDonkey Version 2.9

New functionality from 2.6 to 2.9 version

• added an option to reverse translate a protein sequence to the gene sequence optimised for codon usage in E.coli or S.cerevisie,
• an option to open .phylip alignment file in Alignment Tab.
• added an option for each cloning event to save the clonning scheme to an image file for documentation/presentation. Each cloning event is stored into the cloning hystrory table and this hystory exists while the app is active.

[santoshp]

Hi,

Like Oz, I have also been serial cloner user until Apple decided to stop 32-bit programs. Do you offer the capabilities to do virtual PCR, Gateway/recombination cloning? Not having trial version is such a bummer, can't just purchase a software that does not have extensive documentation/user base without having tried it.

Thank you for your work!

Santosh

[vytarasov]

Hi, there are no options for virtual PCR, Gateway/recombination cloning.

Frankly to say I don't see a sense in virtual PCR. From my experience with PCR in wet lab (more then 20 years) to have a good result of a real PCR you don't need virtual PCR, waste of time. It is just matter of choice of good primers and polymerase preset.

For the documentation you can visit website, it has the same content as HelpBook in the program.

[vytarasov]

The BioLabDonkey Version 3.0

• New, clean graphic view of user interface,
• Bug fixes.

[vytarasov]

New update of BioLabDonkey - Version 3.2

If somebody had a problem with opening .xdna or .dna file I hope in this version they are solved. If not, let me know.

Here is the link to new YouTube video tutorial for Version 3.2 -

Restriction Analysis and Cloning in BioLabDonkey (Plasmid, Linear and Text Maps) - part 1

[vytarasov]

Update of BioLabDonkey - Version 3.5, optimised for macOS Big Sur

Here is the link to the second part of YouTube video tutorial (Version 3.5) -

Cloning and GenBank features in BioLabDonkey (Plasmid, Linear and Text Maps) - part 2

[vytarasov]

Update of BioLabDonkey - Version 3.7

• Additional standard GenBank features for DNA annotation are added to the list,
• The crash during the automatic GenBank features annotation of DNA is fixed,
• Bug fixes in the reads assembly function, the assemble algorithm optimisation,
• Added read ends trimming function to provide an option for improvement of the consensus sequence quality.

GenBank features, RevComplement/Transcribe/ Translate, Find Motifs and ORFs in BioLabDonkey - part3

Primers, DNA sequencing chromatogram, reads alignment and assembly in BioLabDonkey - part 4

[vytarasov]

A new tutorial for BioLabDonkey version 3.7

CG , CpG, Stem Loop content, Codon Optimisation and Silent Insertion/Deletion of Restriction Sites in ORF - part 5

[vytarasov]

Update of BioLabDonkey - Version 3.10 and two tutorials

Genome and Protein Tabs functionality in the BioLabDonkey - part 6

PDB viewer in the BioLabDonkey - part 7

[vytarasov]

Update of BioLabDonkey - Version 4.0

• The DNA and Protein Tabs are redesigned to improve usability.
• The DNA Tabs have interactive graphic view of linear DNA.
• All graphical views (plasmid, ORFs, etc) can be copied/pasted.
• The Plasmid map has options for adjustment of DNA feature positions, restriction site positions and colours.

[vytarasov]

Update of BioLabDonkey - Version 5.2

• User can resize/maximise the window.
• User can open the multiple windows.