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Omicsbox Apps

Extend the functionalities of OmicsBox

OmicsBox Apps and our Developer SDK can be used to extend the functionalities of OmicsBox. With OmicsBox Apps you are able to:

  • Share your own bioinformatics tools or visualizations with the BioBam Community.
  • Create a tool by wrapping a popular command line program to ease your or your colleagues’ research.
  • Connect your software/system with a OmicsBox App that integrates OmicsBox into your existing environment.

Interested in making your own App?

You are more than welcome! Please write us an email to dev@biobam.com and we will provide you with a login to our developer zone and a developer licence key for OmicsBox. Looking forward to getting in touch with you.

Access to the Developer Zone allows you to use all the resources needed to develop OmicsBox Apps.

App Directory

Find here a list of already available tools developed by the BioBam Community and us shortly.

AppTypeManual
MLST
Multi-Locus Sequence Typing (MLST)
Genome Analysis Module
Multilocus Species Typing (MLST) is a nucleotide sequence-based approach of an unambiguous procedure of characterizing isolates of bacterial species using the sequences of internal fragments of (usually) seven house-keeping genes.Author: BioBam Bioinformatics S.L.
Version: 
Release Date: 2019-07-15
Psortb
A prediction tool for bacterial protein subcellular localization
Functional Analysis Module
If you use this tool for your research please cite: PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao, S.C. Sahinalp, M. Ester, L.J. Foster, and F.S.L. Brinkman (2010) Bioinformatics 26(13):1608-1615. For more information please visit: http://www.psort.orgAuthor: BioBam Bioinformatics S.L.
Version: 
Release Date: 2016-05-14
Coding Potential Assesement Tool
This App allow to calculate the coding potential probability for RNA sequences.
Genome Analysis Module
This App allow to use prebuild models or to build new species-specific models from files or from the NCBI datbase in order to assign to each RNA sequence a coding probability score.Author: BioBam Bioinformatics S.L.
Version: 
Release Date: 2017-03-16
Create GenBank Submission Files
This App automatizes the creation of the .sqn file for the NCBI submission.
General Tools
This App allow to combine functional annotations, genome annotations (gff) with its genomics sequence data for direct submission to the NCBI GenBank. The files are created with the help of the tbl2asn tool provided by the NCBI. The App eases the generation of submission files which, once validated, are readily prepared for its submission. This App uses the program tbl2asn available from www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ under the GPL3 license. Author: BioBam Bioinformatics S.L.
Version: 
Release Date: 2016-07-20
Load KEGG Pathways Tool
A tool to load and highlight KEGG pathways by GO annotations. Available only for Academic Subscriptions.
Functional Analysis Module
The "Load KEGG Pathway" tool allows to retrieve metabolic pathways based on the GO terms of an input project. Pathway mapping and highlighting is done via enzyme codes. Obtained pathways are ranked by the number of linked input sequences. The usage of this tool is restricted to academic subscriptions only and is based on a KEGG API subscription agreement between BioBam and Pathway Solutions.Author: BioBam Bioinformatics S.L.
Version: 
Release Date: 2019-03-22