Search Results for "bio process"
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Showing 82 open source projects for "bio process"
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BrightGauge, a ConnectWise solution, was started in 2011 to fill a missing need in the small-to-medium IT Services industry: a better way to manage data and provide the value of work to clients. BrightGauge Software allows you to display all of your important business metrics in one place through the use of gauges, dashboards, and client reports. Used by more than 1,800 companies worldwide, BrightGauge integrates with popular business solutions on the market, like ConnectWise, Continuum, Webroot, QuickBooks, Datto, IT Glue, Zendesk, Harvest, Smileback, and so many more. Dig deeper into your data by adding, subtracting, multiplying, and dividing one metric against another. BrightGauge automatically computes these formulas for you. Want to show your prospects how quick you are to respond to tickets? Show off your data with embeddable gauges on public sites.
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ConnectWise PSA (formerly Manage) allows you to stop working in separate systems, and helps you build a more profitable business. No more duplicate data entries, inefficient employees, manual invoices, and the inability to accurately track client service issues. Get a behind the scenes look into the award-winning PSA that automates processes for each area of business: sales, help desk, support, finance, and HR.
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iCn3D
Web-based protein structure viewer and analysis tool
"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d. iCn3D synchronizes the display of 3D structure, 2D interaction, and 1D sequences and annotations. Users' custom displays can be saved in a short URL or a PNG image. The complete package of iCn3D including Three.js and jQuery is in the directory "dist" after you get the source code with the "Code"... -
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a... -
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes... -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis... -
Don’t settle when it comes to managing your clients’ IT infrastructure. Exceed their expectations with ConnectWise RMM, our MSP RMM software that provides proactive tools and NOC services—regardless of device environment. With the number of new vulnerabilities rising each year, smart patching procedures have never been more important. We automatically test and deploy patches when they are viable and restrict patches that are harmful. Get better protection for clients while you spend less time managing endpoints and more time growing your business. It’s tough to locate, afford, and retain quality talent. In fact, 81% of IT leaders say it’s hard to find the recruits they need. Add ConnectWise RMM, NOC services and get the expertise and problem resolution you need to become the advisor your clients demand—without adding headcount.
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this address: https... -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
... that all files are the version used in the analysis. Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually. -
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Characterisation of fungal fraction in metagenomic surveys, with high end-user flexibility in terms of database creation and customisation.
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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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MSP2MGF
Convert MSP files to MGF files - Only you know why
...: /? displays help information /f anything following is a file you want to process. Things you should know: Change what things in the MSP get mapped into a new name in the MGF in Settings. Anything not on the mapping list is mapped through unaltered. And if this doesn't mean anything to you then this probably isn't the app for you -
Chat with your business data with Looker. More than just a modern business intelligence platform, you can turn to Looker for self-service or governed BI, build your own custom applications with trusted metrics, or even bring Looker modeling to your existing BI environment.
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LoopMatcher
Find sequence-specific stem-loops in FASTA and GenBank files.
... to process large sequences. * Currently, this version only runs in Windows x64. -
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HyLiTE
Hybrid Lineage Transcriptome Explorer
... homeolog over another is extremely challenging, particularly on a whole-genome scale. HyLiTE automates this process, and allows gene expression patterns to be explored even in very complex allopolyploid species. -
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MaxBin
An automatic tool for binning metagenomics sequences
... or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.7. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. -
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MGF2MGF CH
Convert mgf mass values to their nearest elemental formula
... drag and drop mgf files onto the window, or pass filenames though a command line argument. Command line arguments: /? displays help information /w runs in windowed mode (the thing you are looking at now) /f anything following is a file you want to process. Things you should know: The elemental composition is not a sophisticated calculation. -
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HSRA
Hadoop spliced read aligner for RNA-seq data
... is a distributed computing framework for scalable Big Data processing. HSRA currently supports single-end and paired-end read alignments from FASTQ/FASTA datasets. Moreover, our tool uses the Hadoop Sequence Parser (HSP) library (link above) to efficiently read the input datasets stored on the Hadoop Distributed File System (HDFS), being able to process datasets compressed with Gzip and BZip2 codecs. -
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Root Phenotyping Suite
Three different software tools for phenotyping plant root images
... scanning or by 3D digital camera imaging. The software provides a robust, efficient and accurate means of phenotyping of roots, by detecting individual root tips and classifying them as belonging to a primary or lateral root. RootGraph is a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits. -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
.... Currently CSBB provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience. -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http...
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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... -
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BOWS
Bioinformatics Open Web Services
BOWS is a generic system based on Web Services which allows programmatic access to applications running on HPC clusters. BOWS allows incorporation of several independent applications since programmers can install them in HPC clusters in any programming language. The lonely requirement is to write a script named “arrow” which calls BOWS back-end services periodically in order to check for new processes and their required parameters. If a new process is found, the “arrow” script should change... -
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Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
Fast Neurite Tracer (FNT) is a tool for semi-automated neurite tracing. FNT can handle big imaging data such as fMOST data. It can also process other types of light imaging data in general. FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported... -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We... -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in... -
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iCAS - An Illumina Clone Assembly System
An Illumina clone assembly system using SOAPdenovo and ABySS
Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting... -
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GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
The NGS TOOLBOX is a collection of simple open source Perl scripts that perform basic analyses and processing steps using next generation sequencing (NGS) datasets. Each tool is designed to ensure convenient and intuitive usage. Installation and usage does not require any bioinformatics skills. All scripts work out-of-the-box. Advanced users may use the command line based Perl scripts to build automated sequence analyses/processing pipelines. If you use the NGS TOOLBOX you for publication...