BioLabDonkey is a program for macOS. It was written from scratch in Swift (version 5) programming language.
The program aimed at researches in the molecular biology field for use in their everyday routine work. The program is a suite of the bioinformatic tools for the analysis of DNA, RNA, and protein sequences, as well as images of gels, blots, cells and colonies. It also provides a set of useful calculators for molecular biology.
The user interface was developed around a minimalistic design and ease of use, such as:
– direct access to functions in less than three clicks
– essential functionality with a minimum of settings
– minimisation of windows (uncluttered screen)
The program has following functional blocks: DNA, Genome, Protein, PDB-Viewer, RNA-seq, Alignment, Gel/Blot/Cells/Colonies and Calculators/Info. Besides the standard molecular biology file formats BioLabDonkey reads files created by Serial Cloner(.xdna), DNA Strider(.xdna) and ApE (.ape) programs.
The program includes custom algorithms for:
– the protein/DNA sequences alignment
– protein secondary structures prediction
– RNA-seq differential expression
In contrast to the Needleman-Wunsch algorithm, the custom algorithms provide correct alignment independent of the size of the sequences indels. These custom algorithms are faster than the Needleman-Wunsch algorithm for large sequences having high homology.
The custom protein secondary structures prediction algorithm is based on patterns analysis of alpha helices, beta strands and turns. The default database of patterns was generated from publicly available pdb structures. Users can also create their own custom databases from pdb files in addition to the default database, and this is most useful when the proteins of interest are similar to the proteins used to make the database, for example from pdb files of the same protein family, protein location (membrane/cytoplasm) or environment (halophilic, mesophilic, thermophilic).
The method used for calculating RNA-seq differential expression between two samples can be performed for selected genes without alignment of reads to the genome or de novo transcriptome assembly. It requires only the DNA sequences of the selected genes.
Acknowledgement I am grateful to Mike Dyall-Smith for help in developing the program and correcting the Help book.
The features of BioLabDonkey can be seen here – BioLabDonkey Features
BioLabCalculators is app for iPhone. This app provides a set of useful calculators and converters for molecular biology. It also includes a colonies counter. The photo of a Petri dish can be directly taken by iPhone camera or imported from the iPhone photo library.
The provided calculators and converters: Dilution calculator, Molarity calculator, Ligation calculator, SDS PAG calculator, Ammonium sulfate calculator, Bacteria growth calculator, Nucleic acid OD calculator, Nucleic acid amount converter, Protein amount converter.
The features of BioLabCalculators can be seen here – BioLabCalculators Features
The page to write feedback about BioLabDonkey and BioLabCalculators (bugs and user interface complains, suggestions and etc.) is here – Feedback