Search Results for "mind-mapping"
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Showing 13 open source projects for "mind-mapping"
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Croizat
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach. -
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relax
Molecular dynamics by NMR data analysis
...Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
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GromacsProSuite
Graphical User Interface for Gromacs
...Beyond simulation execution, it includes advanced trajectory processing and analysis tools such as RMSD, RMSF, SASA, clustering, PCA, hydrogen-bond analysis, Ramachandran plots, and FEL mapping. With integrated visualization and plotting utilities, it offers a unified platform for researchers, educators, and students to perform complete MD workflows efficiently and reproducibly. Our Goal is to bring MD simulations to every biologist's toolkit. -
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the... -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
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openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of... -
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Spatio-temporal simulation environment (STSE) is set of tools used to perform spatio-temporal simulations, dedicated mainly to biological systems. Main development language is Python. Tools are currently based on: EPD, VTK, qhull, openalea, PlantGL.
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
...Potential false positives arising from spurious alignments are filtered out via a semi-supervised anomaly detection strategy based on logistic regression. Multiple mapping reads with a unique location after filtering are rescued and reallocated to the most reliable candidate location. FineSplice requires Python 2.x (>= 2.6) with the following modules installed: pysam (http://code.google.com/p/pysam/) and scikit-learn (http://scikit-learn.org/). For further details check out our publication: Nucl. ... -
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Tuque
Tools for mapping RNA-Seq reads to eukaryotic genomes
Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals -
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Webapp
A web interface to the SnowyOwl gene prediction pipeline
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A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.
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This program has been written having in mind to create an useful tool to evaluate the Motor Evoked Potentials (MEPs) generated by Transcranial Magnetic Stimulation (TMS) and recorded with the program "Signal" (version 2.xx).
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