Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse
Let me know if any application is missing from the list.
Eclipse
PubCurator
PubCurator is a biomedical text mining platform and validation helper built on top of Eclipse RCP.
LabImage
LabImage platform offers a variety of modules for any user looking for comprehensive bio-imaging software with a workflow-guided approach and an easy way of working.
Compass
Immunoassay analysis tool from Cell Biosciences.
KNIME
KNIME is open source workflow and data mining platform built on top of Eclipse platform. KNIME currently provides broad range of chemoinformatics and bioinformatics tools.
SBSIVisual
SBSIVisual is a desktop application whose provides easier way to run parameter estimation jobs for systmes biology models.
Edinburgh Pathway Editor
EPE is a visual editor designed for annotation, visualisation and presentation of wide variety of biological networks, including metabolic, genetic and signal transduction pathways.
Bio-PEPA
Bio-PEPA Workbench is an implementation of Bio-PEPA langugae which allows modellers to write models in the Bio-PEPA language and to animate them using stochastic simulation.
Bioclipse
Bioclipse provides advanced functionality in fields such as cheminformatics, bioinformatics, semantic web, spectrum analysis, drug discovery, safety assessment, and general chemistry education.
ClustScan (the Cluster Scanner)
ClustScan can analyse the large amounts of data produced by sequencing projects (genome and metagenome data sets) and can generate good predictions of the most likely chemical products from these gene clusters, allowing identification of interesting clusters.
BioUML
BioUML is designed as a common purpose framework for systems biology providing formalized graphic notation to describe the structure and function of biological systems, their visualization and simulation as well as access to databases with relevant experimental data.
NetBeans
Quantitative Biology Tool
QBT provides users a convenient way to define, visualize, annotate, and simulate biological systems of interest.
BioCAD
BioCAD is an platform for bio-network inference and analysis. BioCAD provides effective inference by incorporating various relevant information sources.
Bio-SPICE
Bio-SPICE is an integrated and modular platform for modeling and simulation of spatio-temporal processes in living cells. It can be used for computational and mathematical modelling of multi-scale bio-molecular systems.
BiologicalNetworks
BiologicalNetworks platform allows querying and mapping over a large number of biological databases related to transcriptional regulation, pathways, microarray and proteomic experiments, 3D structures etc.
Gephi
Gephi is an open-source software for visualizing and analyzing large networks graphs of all kinds including biological networks.
Instant JChem
Instant JChem is a desktop application for scientists to manage and work with chemical structures and data using local and shared databases.
Visual Acorn
Acorn is a web server for constraint based modeling of genome-scale metabolic reaction networks.
GenBeans
GenBeans is a multiplatform interactive molecular biology software for DNA analysis.
ChIpInspector
ChipInspector is tool for high quality microarray data analysis and it works with data from exon-, tiling- or gene expression-arrays from vendors like Affymetrix, Illumina or Agilent.
This post is tagged: Eclipse, NetBeans
19 Responses to “Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse”
Latest Tweets
-
Dear Entrepreneur, CXO of unknown start-up with uncertain business model, be grounded and humble. cheersFebruary 10, 2012 at 2:53 am -
Apache Giraph, a framework for large-scale graph processing on Hadoop, reaches 0.1 milestone http://t.co/ymaoSXtTFebruary 10, 2012 at 1:57 am
-
Got this today, nice collection of Studio Ghibali Songs. Yeee http://t.co/mtauzVI7February 10, 2012 at 1:46 am
Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/b4N8T9 #fisheye
Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/b4N8T9
Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/b4N8T9 #science
@rvijapurapu thanks for the pointer, here is the list http://goo.gl/v5nc
RT @abhsihektiwari: Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/c3J0ZO
Nice overview, thanx!
I find it also notable that all this software is written in Java, and, licensing permitting, things can be combined… it would have been, therefore, useful to include license information, as it is the Open Source nature of many of these projects that provide solid shoulders to build on… these products are *not* the final thing, but just the next step in a scientific computing desktop.
Otherwise, there are many dimensions that one could further explore: support for Open Standards, ability to do remote and/or cloud computing, or what underlying 3rd-party libraries are being used by these bioinformatics desktop environments.
Thanks for you comment Egon. I see where you coming from, and I agree that licensing is a major bit. My idea was to just put some example from here and there to show up that Eclipse and Netbeans are used for similar kind of tasks. That was technical side of story. After that, I guess what you are saying is more valuable. That also reminds me the SWT implementation is proprietary and how much of that should be considered as reason that more people are using Netbeans just to avoid the mix up of different licenses?
RT @sysbio: Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/b4N8T9 #fisheye
Platform comparison Systems Biology and Bioinformatics: NetBeans vs Eclipse – http://bit.ly/9yhjFS
RT @sysbio Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/b4N8T9 #fisheye
RT @monacotoni: Platform comparison Systems Biology and Bioinformatics: NetBeans vs Eclipse – http://bit.ly/9yhjFS
Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/bZc9p4 Science.alltop
RT @sysbio Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse http://bit.ly/b4N8T9 #fisheye
Interesting list of Biology and Bioinformatic projects built on Eclipse and Netbeans http://bit.ly/9lLUo7
Nice overview of #Eclipse #RCP and #Netbeans based #bioinformatics and #systemsbiology platforms http://is.gd/f5qJX via @abhishektiwari
Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse :::http://bit.ly/9yhjFS
2 more Eclipse RCP apps
Pubcurator
https://sourceforge.net/projects/pubcurator/
and
http://www.labimage.com/ – a commercial Eclipse RCP image analysis platform
Thanks Richard for you comment. I just updated the list based on your input.
Updated list Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse, Eclipse leads the numbers now – http://goo.gl/v5nc