The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
Bioclipse uses a plugin architecture that inherits a state-of-the-art plugin architecture, functionality, and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment, and more.
Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality.
Key Features
- Bioinformatics:
- Manage and analyse biological sequences (DNA, RNA, and protein).
- Relies on BioJava to provide core bioinformatics functionality and a graphical editor for sequence alignments.
- Clients for web services.
- Plugin architecture based on Eclipse.
- Cheminformatics in Bioclipse is mainly based on the Chemistry Development Kit (CDK), and contains a framework for managing and analyzing chemical compounds. It supports:
- Process large collections of molecules in tables.
- Calculation of various types of property.
- Editing in 2D.
- Pharmacology and drug discovery.
- Advanced tools for interacting with semantic web resources.
- Facilitates working with decision support systems.
- Rich client and takes full advantage of networked resources, such as databases and interoperable Web services, XMPP services.
- Site-of-metabolism prediction.
- Semantic web functionality.
- Browsing of large compound collections.
- Editing of chemical structures.
- Scripting language (Bioclipse Scripting Language, or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others.
- Platform independent.
Website: sourceforge.net/projects/bioclipse
Support: Blog
Developer: The Bioclipse Project
License: Eclipse Public License
Bioclipse is written in Java. Learn Java 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 |
| Scanpy | Scalable analysis of single-cell gene expression data |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| SeqKit | Fast toolkit for manipulating FASTA and FASTQ sequence files |
| samtools | Manipulate next-generation sequencing data |
| MultiQC | Aggregates results from multiple bioinformatics analyses |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| Foldseek | Fast searching and comparison of large protein structure datasets |
| 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 |
Read our verdict in the software roundup.
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