Search Results for "database tool"
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Showing 55 open source projects for "database tool"
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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.
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Train ML Models With SQL You Already KnowBuild and deploy ML models using familiar SQL. Automate data prep with built-in Gemini. Query 1 TB and store 10 GB free monthly.
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CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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MetRFinder
Detection of Heavy Metal Resistance Genes from Bacterial Proteomes
...The modular architecture supports efficient batch processing, organized output management, and reproducible analyses. Note: A detailed User Tutorial PDF is included with the software package to guide installation, database selection, analysis execution, and result interpretation. -
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FungiRegEx
FungiRegEx
This tool is a web-based search engine for regular expressions in the proteomes, all the information is obtained from the JGI (Joint Genome Institute) database through a scraper for all the available species; therefore this tool only considers fungi organisms. In this version, we use React JS in front-end and NodeJS + Express for back-end. -
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. ... -
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PubChemSR is an MS-Windows-based data search and retrieval tool for the NCBI's public chemical database PubChem. PubChemSR makes it especially straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. The latest version is v3.6.5 (released on 11/07/2020), which is fully compatible with the current PubChem web interface.
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LymPHOS2
LymPHOS2 Web-App
LymPHOS2 is a web-based Application at www.LymPHOS.org containing peptidic and protein sequences and spectrometric information on the PhosphoProteome of human T-Lymphocytes. - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes... -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. -
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AntibiogramJ
AntibiogramJ is a Java program for the reading of antibiogram-images
AntibiogramJ is a Java program for the identification, measurement and categorisation of inhibition zones in antibiogram images captured with any device that incorporates a camera (including digital cameras and mobile phones). Citing AntibiogramJ: A. Alonso, C. Domínguez, J. Heras, E. Mata, V. Pascual, C. Torres, and M. Zarazaga. AntibiogramJ: a Tool for Analysing Images from Disk Diffusion Tests. Computer Methods and Programs in Biomedicine 143:159-169. 2017. DOI:... -
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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. -
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.
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...An updated GenoSuite2 is just released where FDRScore (Jones et al. Proteomics 2009) based strategy is used to integrate results from multiple search algorithms. Prokaryotic Proteogenomic Tool(PPT) is developed as a part of GenoSuite framework. PPT is for finding novel translations in prokaryotic genomes and is dependent on Mass Spectrometry based proteomics data and related genome sequence. Some Key features of the tool are.... (1) Configured for 4 open source algorithms to perform database searching for peptide identification. ...
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A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.
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Taxy is a tool for browsing and quering data organized as a taxonomy. Through the use of plugins it allows to connect to different data sources, such as the NCBI species taxonomy or the catalogue of biomedical services of the EU project ACGT.
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LiDSiM
LImits of Detection SImulation for Microbes
LiDSiM is a tool to estimate the possible influence of error-tolerant database searches and proteogenomic approaches on the amount of unidentified spectra and the ratios of taxonomic relationship of identified spectra in MS/MS studies of microbial proteomes. For more details about LiDSiM and its functioning, please see "Estimating the Computational Limits of Detection of Microbial Non-Model Organisms" Mathias Kuhring and Bernhard Y. -
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
Very simple python script which saves you the pains of counting the amino acids/DNA bases in fasta files from the Uniprot and NCBI RefSeq Database (1, 2). Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices... -
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TUIT
Taxonomic Unit Identification Tool
For the installation instructions please see Wiki page: https://sourceforge.net/p/tuit/wiki/ IMPORTANT: since version 1.0.4.0 TUIT allows to select RDP-like formatted output to improve out of the box compatability with tools, that assume RDP-formatted input. A new field has been added to the properties.xml, please make sure to update it to contain <OutputFormat format="tuit"/> or <OutputFormat format="rdp"/> in the <BLASTNParameters> section. Read our paper in Biotechniques:... -
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
...BiSA can also annotate binding regions of interest with nearby genes. The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results. -
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GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
Note: This version requires additional SQLite database files. Contact the developers to obtain them. Use http://www.integrativegenomics.org/ for the latest data and analyses. GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser. -
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ClinStudyWeb is designed to provide a flexible infrastructure for managing patient and assay data from clinical studies. It uses a plugin system for study-specific web forms and arbitrarily complex test classifiers, and supports XML import/export.
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is-sfe
Information System "Supercritical Fluid Extraction"
Information System "Supercritical Fluid Extraction" has developed as tool for collecting and analyzing the experimental data from various supercritical fluids experiments. The final target is to help to scientists who worked with supercritical fluids to predict some useful properties such as density, solubility etc. In order to calculate molecular descriptors, parse SMILES and another applied purposes is used Chemistry Development Kit (https://sourceforge.net/projects/cdk). -
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BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
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Primer Design Tool
Design PCR primers
A simple tool to design DNA primers for mutagenesis in BGME lab (JHU). Allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them. -
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A tool to visualize, analyze and store genomic positioning data.
