ArticleBMC bioinformatics2009
Bioclipse 2: a scriptable integration platform for the life sciences.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed.
- MolBook UNIPI─Create, Manage, Analyze, and Share Your Chemical Data for Free.Journal of chemical information and modeling · 2023Article
- 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
- 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
- Open source molecular modeling.Journal of molecular graphics & modelling · 2016Review
- Large-scale ligand-based predictive modelling using support vector machines.Journal of cheminformatics · 2016Article
- libChEBI: an API for accessing the ChEBI database.Journal of cheminformatics · 2016Article
- Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.Journal of chemical information and modeling · 2015Article
- Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens.Database : the journal of biological databases and curation · 2015Review
- QSAR DataBank - an approach for the digital organization and archiving of QSAR model information.Journal of cheminformatics · 2014Article
- A rule-based ontological framework for the classification of molecules.Journal of biomedical semantics · 2014Article
- Analysis Tool Web Services from the EMBL-EBI.Nucleic acids research · 2013Article
- Applications of the InChI in cheminformatics with the CDK and Bioclipse.Journal of cheminformatics · 2013Article
- Bioclipse-R: integrating management and visualization of life science data with statistical analysis.Bioinformatics (Oxford, England) · 2013Article
- A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms.PloS one · 2013Article
- Mining collections of compounds with Screening Assistant 2.Journal of cheminformatics · 2012Article
- Workflows for microarray data processing in the Kepler environment.BMC bioinformatics · 2012Article
- CheS-Mapper - Chemical Space Mapping and Visualization in 3D.Journal of cheminformatics · 2012Article
- Computational toxicology using the OpenTox application programming interface and Bioclipse.BMC research notes · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundContemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks.
resultsBioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments.
conclusionBioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today's powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations or retrieval of data. The fact that Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, making it easy to add new algorithms, visualizations, as well as scripting commands. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research.Bioclipse 2 is released under the Eclipse Public License (EPL), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.
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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.