BioLabDonkey, BioIllustrator, BioFileConverter(Mac) and BioLabCalculators(iPhone)

BioLabDonkey is a program for macOS. BioLabDonkey is one time purchase app with lifetime updates including new features. This program is aimed at researches in the molecular biology field for use in their everyday routine work. It 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).

Features:

– Open files with the extensions: .txt, .rtf, .fasta, .fas, .fa, .fsa, .ffn, .fna, .seq, .ape, .gb, .gbk, .ab1, .bldna, .xdna, .dna, .faa, .seq, .gp, .blprotein, .fastq, .aln, .phylip, .blalignment, .pdb, .jpg, .tiff, .png. The program reads files created by Serial Cloner(.xdna), DNA Strider(.xdna), SnapGene(.dna) and ApE (.ape) programs.

– Save files with the extensions: .txt, .rtf, .fasta, .fas, .fa, .fsa, .ffn, .fna, .seq, .gb, .gbk, .ab1, .bldna, .faa, .seq, .gp, .blprotein, .blalignment, .pdf, .eps, jpg, png;

– Transcribe, reverse complement and translate DNA sequence;

– Tm, %GC, Mw, length of selected DNA and protein Mw (average and monoisotopic), length of protein, amino acid composition, protein net charge;

– 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;

– Optimize codons in ORF;

– View GC content, CpG islands and Stem Loops;

– Generate Plasmid, Linear and Text map using feature annotations from genbank file;

– Generate and edit DNA/protein features for genbank/genpept format files;

– Generate DNA features database and perform features annotation;

– Copy/paste the selected DNA sequence with features;

– Cloning of a restricted DNA fragment;

– Find/highlight DNA restriction sites and DNA fragments;

– Genome viewer;

– Virtual DNA gel viewer;

– Multiple alignment and realignment of DNA/RNA/protein sequences;

– Assembly of sequencing reads from .ab1 or txt files;

– Phylogenetic trees;

– Protein/DNA/RNA PDB viewer;

– Prediction of protein secondary structures;

– Reverse translation;

– Protein Hydropathicity/pI plots;

– Protein limited proteolysis;

– Find/highlight protease sites and protein fragments;

– RNA-Seq DE: genes and miRNAs differential expression;

– Calculators 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;

– Image adjustment and labels.

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

BioIllustrator is a one time purchase macOS program with lifetime updates. This app is aimed at scientists, students and amateurs interested in the creation of illustrations for scientific articles, PhD and diploma theses or presentations on various topics of biology.  

The drag-and-drop function of curated templates saves time on creating professional scientific illustrations – no more tedious work creating graphical elements ! The app also provides standard tools for the manipulation of images, texts, geometrical shapes and lines.

The current version of the app contains templates for the following fields of biology: molecular biology, cell biology, microbiology, botany.  Each field is divided to subfields that facilitate the search for specific templates. There are templates of laboratory equipment useful for workflow illustrations. New templates and biological fields will be added regularly with updates of the app.  

Besides the default templates, users can request particular templates free of charge at the app support website. New templates will be included in the following app update.

BioIllustrator templates can be inserted as an image into any image editor or other presentation app. Users can also import custom images (JPG, PDF, PNG, TIFF) or text into the BioIllustrator canvas.     

Illustrations can be saved to the custom file format (.bil extension) for later  editing or can be exported to PDF, PNG, JPG or TIFF files for publication. 

In addition to the templates, the app contains links to open source scientific articles (reviews) selected for each biological filed/subfield. This can assist in the creation of scientifically grounded illustrations as well as in the writing of reports or theses on the corresponding topics.

The BioIllustrator features – BioIllustrator video tutorials

Acknowledgement I am grateful to Mike Dyall-Smith for help in developing this program.

BioFileConverter is an app to convert files often used in molecular biology.

BioFileConverter converts .xdna (from SerialCloner or DNA Strider app), .dna (from SnapGene app) files and .ape (from ApE app) into .gb (GenBank) file. The content of converted GenBank file is formatted according to the specification of the GenBank file format, but it also depends on the content of .xdna or .dna files. For that reason some GenBank format features can be missing in the converted .gb file. BioFileConverter also converts .abi, ab1, fasta/fas/ffn/fna/frn or fastq files into .txt files containing DNA/Protein sequences without any description line.

BioFileConverter is useful for the fast conversion of a set of files at once.

BioLabCalculators is an 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, BioIllustrator, BioFileConverter and BioLabCalculators (bugs and user interface complains, suggestions and etc.) is here – Feedback