CycleCloud Applications
The cloud derives much of its utility from the tools it has to solve problems. Since 2007, CycleCloud has helped clients optimize cloud clusters to run specific applications well. With native support for various applications in life sciences, finance, and insurance, CycleCloud clusters start with the applications needed to run many types of workflows out of the box.
Bioinformatics
| Blast |
BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. |
| GMAP |
A genomic mapping and alignment program for mRNA and EST sequences. |
| HMMER |
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called "profile hidden Markov models". |
| MAQ |
Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. |
| Bowtie |
Bowtie is an ultrafast, memory-efficient short read aligner. |
| RMAP |
RMAP is aimed to accurately map reads from the next-generation sequencing technology. RMAP can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. |
| MrBayes |
MrBayes is a program for the Bayesian estimation of phylogeny. |
Proteomics
| OMSSA |
The Open Mass Spectrometry Search Algorithm [OMSSA] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. |
| X! Tandem |
X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. |
Computational Chemistry
| GROMACS |
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| ROCS |
ROCS is a fast shape comparison application, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. |
Statistics
| R |
R is a free software environment for statistical computing and graphics. |
Miscellaneous
| G95 |
G95 is a stable, production Fortran 95 compiler available for multiple cpu architectures and operating systems. |
| OpenMPI |
An open source message parsing interface. |
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