Search Results for "informatics" - Page 14
Sort By:
Showing 2481 open source projects for "informatics"
View related business solutions-
Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
-
Custom VMs From 1 to 96 vCPUs With 99.95% UptimeLive migration and automatic failover keep workloads online through maintenance. One free e2-micro VM every month.
-
1
DicomReader is a simple Java Dicom files decipher. It handles headers and images within as well; data (headers and pixel-value images) will be saved into ascii clear text files. A pgm version of the image files is also provided.
-
2
Open-source Python software library and GUI desktop environment for direct bioinformatic analysis of mass-spectrometry data through powerful scripting tools and interfaces to many machine data formats, database search engines, and peptide data formats. For a copy of the source code, check out our Github repositories: mzDesktop: https://github.com/MaxAlex/mzDesktop multiplierz: https://github.com/MaxAlex/multiplierz
-
3
GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
4
isiKnock
In silico knockouts for signaling pathways
Signaling pathways are complex and intertwined processes. The perturbation of biological systems can reveal the complicated interplay and dependencies of pathway components. isiKnock is a software to automatically conduct and visualize in silico knockouts for signaling pathways (Hannig et al. 2019). isiKnock predicts the knockout behavior based on the calculation of signal flows at steady state. For an explanation of the concept of in silico knockouts, we refer to Scheidel et al. 2016... -
Veeam Data Platform v13.1 - Get Your Free TrialTry Veeam Data Platform today. Experience the unified platform that's secure by design, portable by default, and proven to recover clean, fast, and anywhere.
-
5
CNVMM
CNVMM performs copy number variations detection
CNVMM specializes in identifying copy number variations (CNVs) when there are repeated sequences in the reference genome. The input file is a single short read mapping result from any short read aligners. However, NNmapper or Bowtie2, which detect all mapping results for multi-reads, are recommended. To use the code, MATLAB installation is required. Mac or Linus system is required. -
6
PanOCT
Pan-genome Ortholog Clustering Tool
PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters. -
7
NNmapper
Perform short reads mapping
NNmapper constructs reference reads library and calculates the Euclidean distances between library reads and query reads. NNmapper can map a query read (1) to the library read that gives the smallest distance (most similar), (2) to the library read that gives the smallest distance while the distance is smaller than a threshold, or (3) all library reads that have distances smaller than threshold. NNmapper has high error-tolerant and is suitable for any read lengths. NN reports all mapping... -
8
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
-
9
RNAfdl
RNA force directed layout
RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings. -
$300 Free Credits to Build on Google CloudPut your $300 in credit toward real workloads, then keep building with free monthly usage for 20+ products. No commitment and no charge until you upgrade.
-
10
MethyMer
Design of specific primer combinations for bisulfite sequencing
MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation... -
11
mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
12
Application to optimize DNA sequences coding protein to put in in the different organizm (f.e. human protein in E.Coli). It proposes the optimal cutting places to connect many shorter fragments into bigger one using ligaze.
-
13
rDock
A Fast, OpenSource Program for Docking Ligands to Proteins and N.Acids
rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages. The full rDock software package requires less than 50 MB of hard disk space and it is compilable in all Linux computers. Thanks to its... -
14
MetExpert is an expert system to assist users with limited expertise in informatics to interpret GCMS data for metabolite identification without querying spectral databases
-
15
Specify Software
Biodiversity Database Platform
Specify is a biological collections and species occurrence database management platform for zoological museums, herbaria and other biodiversity specimen repositories. Specify is supported by grants from the Division of Biological Infrastructure, U.S. National Science Foundation and the State of Kansas. A web browser application, Specify 7, is available on GitHub. In 2015, 450 biological collections worldwide use Specify Software for collections data management. An iPad app, Specify Insight... -
16
EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence. Please download EigenMS.zip file (latest version). Latest version uploaded in October 2017 has a bugfix for single treatment group normalization. Rescaling has been omitted from 2015. EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be...
-
17
Collaborative Computing Project for NMR
Collaborative Computing Project for NMR (CCPN)
The Collaborative Computational Project for NMR (CCPN) provides tools and knowledge to maximise the impact of the biological NMR studies. The CCPN software facilitates data analysis and software integration. The project actively promotes the exchange of knowledge and provides training and best practices for the NMR community. CCPN also has a leading role in the development of a NMR data-sharing standard and coordination of NMR instrumentation proposals for RCUK and BIS. The 28 partners of... -
18
EFO
The Experimental Factor Ontology describing experimental variables
*** Please note this repository is now deprecated as of January 2018. All EFO development and source code has been moved to https://github.com/EBISPOT/efo *** The Experimental Factor Ontology (EFO) available from http://www.ebi.ac.uk/efo is an application focused ontology modeling the experimental factors in ArrayExpress and constructing mappings to multiple existing domain specific ontologies. To submit new terms, features or report bugs please submit a ticket at the following:... -
19
REHUNT
REHUNT (Restriction Enzymes HUNTing)
REHUNT (Restriction Enzymes HUNTing) is a free and open source package implemented in JAVA for providing many useful methods for biological sequence analysis (especially in SNP genotyping) around restriction enzymes. All academic researchers are encouraged to use REHUNT in their studies or to integrate it into their systems and applications. Non-academic users or commercial needs are also welcome to use it. For further information or additional applications, please contact the author... -
20
irayMol
Molecular visualization
Analyses and Interactive visualizations of the structures, functions and actions of biomolecules including molecular surface computation, and protein-ligand interface and protein-ligand docking where the ligand could a small compound, a nucleic acid, membrane and other proteins, written in C++/Qt/openGL/GLSL with more than 125,000 lines of codes. In addition to Qt, the only external library needed is GSL everything else is coded from the scratch. -
21
RDML-Ninja is an editor for qPCR data. It is the reference implementation for the RDML data standard allowing to visualize, edit and reanalyze qPCR data.
-
22
LMAP
Lightweight Multigene Analyses in PAML
Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016) LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics, 17:354. doi: https://doi.org/10.1186/s12859-016-1204-5 -
23
The Wily DNA Editor
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section. -
24
RDML stands for Real-time PCR Data Markup Language and is the standard file format for export, storage and exchange of quantitative PCR (qPCR) data. This project focuses on the development, implementation and enhancement of the RDML file format and its description (XML schema).
-
25
BioRec:Bird Census field data annotation
Recognizing biological data from a notebook.
This project helps to digitize field data for a certain Bird Census method. Namely, bird census based on personal inspection or small (~10 km^2) regions with recording birds' position and behaviour on paper. This project makes it easy to annotate such field data and to make this data available for statistical analysis.