Search Results for "visualisation"

A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data

...You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the user can interactively select the rules to be applied. GroIMP provides classes that can be used in modelling: Turtle commands, further geometrical classes like bicubic surfaces, the class Cell which has been used in the Game Of Life implementation, and so on. ...

This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually.

Visualisation of gene expression data on prokaryotic genomes

The complexity of cellular networks is an outstanding challenge for documentation, visualisation and mathematical modelling. In this project, we develop a new way to describe these networks that minimises the combinatorial complexity and allows an automatic visualisation and export of mathematical (ODE/rulebased) models.

Gene Slider can be used to visualize conservation and entropy of aligned DNA and protein sequences by presenting them as one long sequence logo. The presented sequence logo can be zoomed in and out. It can also display motifs in alignments. A built-in search function can be used to find motifs. Gene Slider is available online on the Bio-Analytic Resource and for download here.

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

Biogranat (Molecular Biology Graph Visualisation and Analysis Tool) is a new tool for the analysis and visualisation of large datasets.

Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis.

SVGMap is an open source web tool to help you in the visualisation of experimental data associated to some graphical representation. More at : 1. Project website http://bg.upf.edu/svgmap 2. Reference : Xavier Rafael-Palou, Michael P. Schroeder, and Nuria Lopez-Bigas SVGMap: configurable image browser for experimental data Bioinformatics 2011 : btr581v1-btr581.

OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing complex queries against the Gene Ontology Database.

Geneview is a visualisation tool to display genetic sequence data stored in nucleic sequence databases like <A HREF="http://www.ncbi.nlm.nih.gov/Genbank/">GenBank</A>.

PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.

SpOK - The Spectrum Organisation Kit, a program for the organisation and visualisation of spectral data written in Java. Sorry - this project is not being continued. All functionality was integrated into the Bioclipse project...

A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).