Applications
Software that can be categorized as ‘Applications’, i.e., not compilers, tools etc. For a full list see the A-Z list.
Bioinformatics
| PACKAGE |
NOTES |
| BCFtools |
Variant call manipulation in BCF (and VCF) files. |
| Bedops |
A fast, flexible toolset for genome arithmetic. |
| Bedtools |
A fast, flexible toolset for genome arithmetic. |
| Bioconductor (in R) |
Tools for analysis and comprehension of high-throughput genomic data |
| Bowtie |
Sequence alignment |
| Bowtie2 |
Sequence alignment |
| bwa |
Burrows-Wheeler Aligner, genome sequence mapper |
| Cufflinks |
Sequence assembly |
| Ensembl Tools |
Varient Effect Predictor script in perl |
| fgwas |
Tool for integrating functional genomic information into a GWAS |
| Gold Suite |
Protein Docking |
| HiCUP |
Genome mapping |
| MEGAN6 |
Tool for studying the taxonomic content of a set of DNA reads |
| SAMtools |
Sequence alignment and mapping tools |
| TADtool |
Hi-C data topological domain analysis |
| tabix |
Generic indexer for TAB-delimited genome position files |
| tophat |
Splice junction mapper |
| vcftools |
Package for working with VCFfiles |
| jellyfish |
A tool for fast, memory-efficient counting of k-mers in DNA. |
Computational Chemistry, Molecular Dynamics
| PACKAGE |
NOTES |
| Gold Suite |
Protein Docking |
| MOE |
Molecular Operating Environment |
| VMD |
Graphical Molecular Visualisation Tool |
Mathematics / Data Analytics
| PACKAGE |
NOTES |
| Anaconda Scientific Python |
A scientific python distribution |
| gauss |
Numerical and statistical computation, visualization and programming |
| IPython Notebook |
Interactive remote execution with web-based viewing of Python (no longer supported, use jupyter notebook) |
| Julia |
Interactive scientific programming language |
| Jupyter Notebook |
Interactive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop) |
| MATLAB |
Numerical computation, visualization and programming |
| R |
Statistical computing and graphics |
| RStudio |
GUI-based development environment for R |
| SAS |
Data analysis and statistical software |
| Stata |
Data analysis and statistical software |
| Mplus |
Data analysis and statistical software |
| MAUD |
General diffraction/reflectivity analysis primarily based on the Rietveld method |
Programming and Development
| PACKAGE |
NOTES |
| Anaconda Scientific Python |
A scientific python distribution |
| Clojure |
Java-based dynamic programming language |
| Compilers – GNU |
gcc, g++ and gfortran |
| gauss |
Numerical and statistical computation, visualization and programming |
| IPython Notebook |
Interactive remote execution with web-based viewing of Python (no longer supported, use jupyter notebook) |
| Jupyter Notebook |
Interactive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop) |
| MATLAB |
Numerical computation, visualization and programming |
| NetBeans |
Java-based IDE |
| NetLogo |
Multi-agent modelling environment |
| R |
Statistical computing and graphics |
| RStudio |
GUI-based development environment for R |
| Singularity |
Containers |
| tensorflow |
Data flow graph processing |
Visualization / Image Processing
Some of the application pages below include instructions on how to run the application on the iCSF GPU node (
jabberwock). Doing so will often give much better graphics performance, making the application feel more responsive and easier to use when viewing large models (e.g., finite element meshes, chemical models, X-Ray tomography 3D datasets etc.) For screenshots of some of these applications please see the
iCSF GPU node page.
| PACKAGE |
NOTES |
| EEGLab |
MATLAB toolbox for EEG/MEG data processing and viz |
| gauss |
Numerical and statistical computation, visualization and programming |
| ImageJ and Fiji |
Image processing (Java) applications. |
| IPython Notebook |
Interactive remote execution with web-based viewing of Python (no longer supported, use jupyter notebook) |
| Jupyter Notebook |
Interactive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop) |
| MATLAB |
Numerical computation, visualization and programming |
| MRIcroGL |
3D GPU Medical Imaging |
| MRIcron |
Medical Imaging |
| NetLogo |
Multi-agent modelling environment |
| VMD |
Graphical Molecular Visualisation Tool |
