ArticleBMC bioinformatics2007
Bioclipse: an open source workbench for chemo- and bioinformatics.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed.
- The evolution of open science in cheminformatics: a journey from closed systems to collaborative innovation.Journal of cheminformatics · 2025Article
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- Development of artificial neural network models to predict the PAMPA effective permeability of new, orally administered drugs active against the coronavirus SARS-CoV-2.Network modeling and analysis in health informatics and bioinformatics · 2023Article
- Advances in Predictions of Oral Bioavailability of Candidate Drugs in Man with New Machine Learning Methodology.Molecules (Basel, Switzerland) · 2021Article
- Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.Antimicrobial agents and chemotherapy · 2020Article
- Article
- Novel Computational Approach to Predict Off-Target Interactions for Small Molecules.Frontiers in big data · 2019Article
- Structure⁻Activity Relationship and Molecular Docking of Natural Product Library Reveal Chrysin as a Novel Dipeptidyl Peptidase-4 (DPP-4) Inhibitor: An Integrated In Silico and In Vitro Study.Molecules (Basel, Switzerland) · 2018Article
- PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.Journal of cheminformatics · 2018Article
- Computational Analysis of LOX1 Inhibition Identifies Descriptors Responsible for Binding Selectivity.ACS omega · 2018Article
- The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.Journal of cheminformatics · 2017Article
- SPLASH, a hashed identifier for mass spectra.Nature biotechnology · 2016Article
- Building a virtual ligand screening pipeline using free software: a survey.Briefings in bioinformatics · 2016Review
- XMetDB: an open access database for xenobiotic metabolism.Journal of cheminformatics · 2016Article
- Large-scale ligand-based predictive modelling using support vector machines.Journal of cheminformatics · 2016Article
- Design, synthesis, in silico toxicity prediction, molecular docking, and evaluation of novel pyrazole derivatives as potential antiproliferative agents.EXCLI journal · 2016Article
- Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.Journal of chemical information and modeling · 2015Article
- The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools.Brain imaging and behavior · 2014Article
- Fusing dual-event data sets for Mycobacterium tuberculosis machine learning models and their evaluation.Journal of chemical information and modeling · 2013Article
- Multiphasic analysis of whole exome sequencing data identifies a novel mutation of ACTG1 in a nonsyndromic hearing loss family.BMC genomics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework.
resultsBioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction.
conclusionBioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.