Cupcake was originally developed as a e-lab notebook that includes various advanced function like timers, voice and video recorder, sample tracker and many more. Recently, it has been extended to management of proteomics job submission and metadata, specifically in SDRF format. It combined the typical proteomics MS job submission for MS experiment to a facility with an SDRF metadata builder ensuring that any job submitted to the facility would also have a compliant SDRF file.
Cinder is a web application that allow users to upload their proteomics analysis results and index them for searching. The application can be used in conjunction with other proteomics analysis tools like Curtain and CurtainPTM where it would automatically import data from submitted Curtain or CurtainPTM links as well as the volcano plot and all its settings.
Sequal can be used for reading and formatting protein sequences with and without modifications whether or not they are placed as suffix or prefix to the amino acid residue. With it there is also a minimal support for certain Mass Spectrometry related task within the package.
The package is simple and can either choose to query data as fasta or in tabulated text form with or without all isoforms. For a synchronous workflow, the tool use Python requests module while aiohttp is used in case of asynchronous integration.
The package is a direct adaptation of the same algorithm used by a plugin of the same name in Perseus proteomics analysis suite for calculation of copy number based on amount of histone within the sample.
The package use gene ids or uniprot accession ids as input to retrieve refseqgene record from NCBI and then use the exon information to build a fasta library of all possible combination of exons with or without introns.