Search Results for "model-builder"
Sort By:
Showing 112 open source projects for "model-builder"
View related business solutions-
$300 Free Credits for Your Google Cloud ProjectsLaunch your next project with $300 in free Google Cloud credits—no strings attached. Test, build, and deploy without risk. Use your credits across the entire Google Cloud platform to find what works best for your needs. After your credits are used, continue with always-free tier services. Only pay when you're ready to scale. Sign up in minutes and start exploring.
-
Atera - an All-in-one platform for IT managementYour IT essentials, integrated & elevated. Take your IT management from automated to autonomous, download Atera's agent to start your free trial!
-
1
AlphaGenome
Programmatic access to the AlphaGenome model
The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. AlphaGenome achieves state-of-the-art performance across a range of genomic prediction benchmarks, including numerous diverse variant effect prediction tasks. -
2
BioNeMo
BioNeMo Framework: For building and adapting AI models
BioNeMo is an AI-powered framework developed by NVIDIA for protein and molecular generation using deep learning models. It provides researchers and developers with tools to design, analyze, and optimize biological molecules, aiding in drug discovery and synthetic biology applications. -
3
relax
Molecular dynamics by NMR data analysis
...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. -
4
PhysiCell
physics-based multicellular simulator
PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations. -
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.
-
5
NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
-
6
SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
7
The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. ...
-
8
TASSEL
TASSEL is a bioinformatics software package
TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics. -
9
GroIMP
Growth-grammar related Interactive Modelling Platform
...GroIMP provides classes that can be used in modelling: Turtle commands, further geometrical classes like bicubic surfaces, the class Cell which has been used in the Game Of Life implementation, and so on. The outcome of a model is visualised within GroIMP. In the visual representation of the model output, users can i -
Compliant and Reliable File Transfers Backed by Top Security CertificationsStop relying on non-certified, legacy file transfer tools that creak under the weight of modern security demands. Get full audit trails, advanced access controls and more supported by an award-winning team of experts. Start your free 25-day trial today.
-
10
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 Children's National Medical Center. ... -
11
MSP Builder 2
Converts text files (such as csv, tsv, txt) to MSP files
Take a list from a search and how do you use that as a search. Answer: As an MSP file. But how do you make one? Answer: With this app. Convert your csv etc files to MSP. You define the relationship (the mapping) and take it from there. Includes a couple of examples. -
12
The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.
-
13
SMTracker (v1.5, v2.0)
A tool for analysis and visualization of single-molecule tracking data
SMTracker v2.0 is a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualising and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by- track basis. Diffusion parameters and motion behaviour is analysed by several methods: a) by a Gaussian mixture model ,or b) by using the cumulative probability distribution of square displacements, c) Mean-Squared displacement fits, d) by Jump Distance analysis. It also includes exploratory tools to visualise single trajectories or dynamic heat maps. -
14
Antimony
Antimony is a human-readable, human-writable model definition language
Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats. -
15
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... -
16
CBMPy
PySCeS Constraint Based Modelling
...Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. CBMPy supports user interaction via: - interactive console or as a library for advanced use - GUI, visual representation of the model, analysis methods - a SOAP based webAPI exposes high level functionality via web services -
17
PBTK Optimizer
Application for optimization of parameters in PBTK models
...This tool was designed to optimize a user-specified list of parameters to a user-specified PBTK model. The user also controls validation data and optimization algorithms. In addition to optimized parameters, the tool outputs statistical information about the fit of the optimized model. -
18
RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI:...
-
19
Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.
-
20
BEMoDA
Dissolution profile comparison Model Dependent-Independent Approach
Dissolution profile comparison (Biowaiver aid) Model Dependent-Independent Approach scripts for in-vitro dissolution profile comparison as proposed by Sathe et al. in 1996 (Sathe PM, Tsong Y, Shah VP. In-vitro dissolution profile comparison: statistics and analysis, model dependent approach. Pharm Res. 1996 Dec;13(12):1799-803) and Tsong et al. in 1996 (Tsong Y, Hammerstrom T, Sathe P, Shah VP. (1996) Statistical Assessment of Mean Differences between Two Dissolution Data Sets, Drug Info. ... -
21
This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
-
22
ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML).
-
23
CognitionMaster
object-based image analysis framework
Wienert S, Heim D, Kotani M, Lindequist B, Stenzinger A, Ishii M, Hufnagl P, Beil M, Dietel M, Denkert C, Klauschen F. CognitionMaster: an object-based image analysis framework. Diagn Pathol 2013, 8:34 -
24
nmr-nessy
NMR relaxation dispersion spectroscopy analysis software
...The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models. -
25
Arabidopsis Motif Scanner
Scanner of cis-regulatory elements in Arabidopsis genome
...Cis-acting en-hancers and silencers appear to have key roles in regulating gene expression. Arabidopsis Motif Scanner was design to build gene networks by identifying the cis-regulatory elements position in the model plant Arabidopsis thaliana and by providing an easy interface to evaluate gene relations.
