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Showing 134 open source projects for "set"
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure stable performance during parallel processing. ... -
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In addition to computing co-expression clusters, Maccu fishes potential co-expressed genes for a given bait set. All results can be further processed via graph-level operations so that we can compare graphs based on different reference data.
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
kSNP4 identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs. SNP discovery is based on k-mer analysis, and requires no multiple sequence alignment or the selection of a reference genome, so kSNP4 can take 100's of microbial genomes as input. A SNP locus is defined by an oligo of length k surrounding a central SNP allele. -
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The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR....
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Enterprise-grade ITSM, for every businessFreshservice is an intuitive, AI-powered platform that helps IT, operations, and business teams deliver exceptional service without the usual complexity. Automate repetitive tasks, resolve issues faster, and provide seamless support across the organization. From managing incidents and assets to driving smarter decisions, Freshservice makes it easy to stay efficient and scale with confidence.
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Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.
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genppi
GENPPI: standalone software for creating protein interaction networks
...Also, It allows the user to define how he intends to explore the PP and CN characteristics through various parameters that let on the creation of customized interaction networks. For instance, one can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice what set of genomes he is going to study. Please, to obtain the software and tutorials access: https://genppi.facom.ufu.br -
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The Simplest Manual Counter
Manual counter with the keyboard or the mouse on images
The only open source counter to count any items the simplest and easiest way with the keyboard, or the mouse specifically on images. After associating a key to each item, or a predefined graphical symbol for images, pressing the key or clicking on the image increments its associated counter, and displays (for the images) the symbol at the mouse's pointer location. Such a project is so simple a child could use it! -
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GroIMP
Growth-grammar related Interactive Modelling Platform
Important: Groimp migrates to Gitlab. 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... -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
MAGeCK2 is here: https://github.com/davidliwei/mageck2 Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at... -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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VMS Draw
user-friendly access to the latest computational spectroscopy tools
...Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set of methods for computational spectroscopy. -
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geostd is an open-source set of restraints for molecules involved in macromolecular structure refinement. The restraints reduce the number of variables making the solution of protein structures a more tractable process.
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gsasnp2
PubMed ID: 29562348 / DOI: 10.1093/nar/gky175
* GSA-SNP2 is a successor of GSA-SNP (Nam et al. 2010, NAR web server issue). GSA-SNP2 accepts human GWAS summary data (rs numbers, p-values) or gene-wise p-values and outputs pathway genesets ‘enriched’ with genes associated with the given phenotype. It also provides both local and global protein interaction networks in the associated pathways. * Article: SYoon, HCTNguyen, YJYoo, JKim, BBaik, SKim, JKim, SKim, DNam, "Efficient pathway enrichment and network analysis of GWAS summary data... -
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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MORPHEUS for Fiji
A tool for unbiased and reproducible cell morphometry in Fiji/ImageJ2
...Specifically, MORPHEUS works with sampling distributions to learn—in an unsupervised manner and by a non-parametric approach—how to recognize the cells suitable for subsequent analysis. Afterwards, the algorithm performs the evaluation of the most relevant cell-shape descriptors over the full set of detected cells. Optionally, also the extraction of nucleus features and a double-scale analysis of orientation can be performed. The whole algorithm is implemented as a one-click procedure, thus minimizing the user intervention and the ensuing biases and errors of human origin. By this way, MORPHEUS is intended to be a useful tool to face the issue of reproducibility in bioimage analysis. -
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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PepDistiller
A software to validate the peptide identifications of Mascot results
...By including the number of tryptic termini, and integrating a refined false discovery rate (FDR) calculation method, we demonstrated the improved sensitivity of peptide identifications obtained from semitryptic search results. Based on the analysis of a complex data set, approximately 7% more peptide identifications were obtained using PepDistiller than using MASCOT Percolator. Moreover, the refined method generated lower FDR estimations than the percentage of incorrect target (PIT) fixed method applied in Percolator. Using a standard data set, we further demonstrated the increased accuracy of the refined FDR estimations relative to the PIT-fixed FDR estimations. ... -
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ProteoWizard development moved to GitHub in 2018. The ProteoWizard Library is a set of software libraries and tools for rapid development of proteomics data analysis software. The libraries are cross-platform and built from the ground up using modern C++ techniques.
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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 utilized for any -omic platform. ...
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. ... -
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The Ontology for Biomedical Investigations (OBI) provides an ontologically well-engineered, integrated set of generic and domain-specific terms for use by different communities, from across the biosciences, using any of a variety of technologies.
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MPprimer
a program for reliable multiplex PCR primer design
Background: Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template using more than one primer set (comprising a forward primer and a reverse primer) in one tube, has been widely used in clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility. ... -
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected Square method (OMES), McLanhlan Based Substitution Correlation (MCBASC), Direct-coupling analysis (DCA) and logR. ... -
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Mass Difference Calculator
Mass Difference Calculator with a Graph for MassLynx data
A Mass Difference Calculator with a graph for MassLynx. Bring in a text file with reference masses and then paste in or browse in another file with a list of mass/intensity pairs. Then look at the best matching points and see what the difference between reference and data comes out as. This is a companion app to ResCalc3 -
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PALM
Probabilistic natural mapping for gene based association study.
PALM is a software that conducts gene-based association analysis. PALM exploits Hidden Markov Models (HMM) to capture the inner genomic structures. Then, unique gene features (termed "palm prints") are extracted for each gene set by calculating the natural gradient. Then palm-prints are tested with chi-square significance test. -
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CorNetMap
A tool for Gene Expression Correlation Network
Capabilities of CorNetMap: 1. Read data as tab-delimited text file. Can be used for analysis of any data set beyond gene expression. 2. Capable of both two-dimensional and multidimensional data analysis. 3. Calculate Pearson correlation and cross-correlation for analysis data with phase difference. 4. Generate correlation Heat-map and draws network map. 5. Save correlation data as text file. How to use and doccumentation: https://sourceforge.net/projects/cornetmap/files/Documentation_corNetMap.pdf Sample data for testing: https://sourceforge.net/projects/cornetmap/files/Test%20Data/ Citation: Cite CornetMap as " Khaund, A. ...
