InterMine is an open source data warehouse system for the integration and analysis of biological data.
It’s a software system that you can install on your own servers to make data available on the web.
The software is released under an open source license.
Key Features
- Dynamic data tables – easily drill down into data. It’s easy to filter data, add additional columns, navigate to report pages.
- Work with single items (objects) and multiple items (lists):
- Object: A single item in the database (this can be anything, a gene, protein or binding site for example).
- List: Multiple items of the same type. For example, a list of genes or a list proteins.
- Run queries in many languages.
- Four search tools are available:
- Keyword Search : A simple search box for looking up names, symbols identifiers or keywords.
- Template Searches : A pre-defined search which provides a simple form with one or more variables for you to define (defaults are always provided so you can see exactly what the template does).
- The Query Builder : An advanced query building tool – you can use this to construct your own searches. You can even turn them into your own template searches.
- Region Search: A tool for looking at genomic regions and the features they contain. Allows you to upload a set of regions and search for features mapped to these regions.
- Supported formats:
- Chado
- GFF3
- FASTA
- GO & gene association files
- UniProt XML
- PSI XML (protein interactions, Protein Structure Initiative)
- InParanoid orthologs
- Ensembl
Website: intermine.org
Support: Documentation, GitHub Code Repository
Developer: University of Cambridge
License: GNU Lesser General Public License (LGPL) version 2.1
InterMine is written in Java and JavaScript. Learn Java with our recommended free books and free tutorials. Learn JavaScript with our recommended free books and free tutorials.
Related Software
| Bioinformatics Tools | |
|---|---|
| Bioconductor | Analysis and comprehension of high-throughput genomic data |
| Biopython | Tools for biological computation written in Python |
| UGENE | Set of integrated bioinformatics software |
| BioPerl | Perl tools for computational molecular biology |
| GROMACS | Versatile package to perform molecular dynamics |
| IGV | High-performance visualization genome browser tool |
| GATK | Genomic analysis toolkit focused on variant discovery |
| BioJava | Provides Java tools for processing biological data |
| InterMine | Integrate biological data sources |
| bedtools | Powerful toolset for genome arithmetic |
| EMBOSS | The European Molecular Biology Open Software Suite |
| BLAST | Algorithm for comparing primary biological sequence information |
| Galaxy | Web-based platform for data-intensive computational research |
| minimap2 | Versatile sequence alignment program |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| samtools | Manipulate next-generation sequencing data |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| FastQC | Quality control tool for high throughput sequence data |
| SPAdes | Versatile toolkit for assembling and analysing sequencing data |
| GenomeTools | Collection of bioinformatics tools |
| AliView | Alignment viewer and editor |
| mothur | Analyze microbial communities |
| Bandage | Visualising de novo assembly graphs |
| cramino | BAM/CRAM quality evaluation |
| abPOA | Adaptive banded Partial Order Alignment |
| Taverna Workbench | For designing and executing bioinformatics workflows |
| geWorkbench | Software platform for integrated genomic data analysis |
| Bioclipse | Rich-client platform chemistry and biology workbench |
Read our verdict in the software roundup.
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