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Error to trace to log to deploy. One click. No SSH.
Catch the cause before the pager goes off.
AppSignal links every error to the trace, the trace to the log, the log to the deploy that shipped it.
PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.
This is a c-library that provides tools for advanced
analysis of electrophysiological data. It features
denoising, unsupervised classification, time-frequency
analysis, phase-space analysis, neural networks, time-warping and
more.
NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
Software to identify cavities and crevices in proteins. The goal is to be able to take a protein structure, and to differentiate between five different types of environments for each residue: buried, surface, interfacial, cavity, or crevice.
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Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.
Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
PyMOL Plugins aims to provide many plugins for the PyMOL software.
You can find further informations about PyMOL on this website:
http://www.pymol.org/
NumericalFISH is a bioinformatics graphical tool for easy analysis of BLAST or BLAT results, especially aimed at the study of duplications or segmental duplications.
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Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).
BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.
H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
A database and a web front end for physiologic data on animal feeding, developed with PostgreSQL and Django at NESCent (http://www.nescent.org) for Mammalian Feeding Working Group (http://www.feedexp.org).
Current development of the codebase is on Github at http://github.com/NESCent/feedingdb.
mmView is the web based viewer of macromolecular Crystallographic Information File (mmCIF) format. Online ready-to-use version is available at http://ich.vscht.cz/~cechp/mmcif/ or http://ich.vscht.cz/projects/mmview/
The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
Free software tools released by the Virtual Institute for Microbial Stress and Survival, including WIST (a toolkit for LIMS development) and PCAPStore (a file repository for LIMS).
Metmask has moved to github http://github.com/hredestig/metmask
Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.
--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE--
The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.
MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.
SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.