Search Results for "tiny-workflow" - Page 2
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Showing 118 open source projects for "tiny-workflow"
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AMBIT:Chemical Structure DB&Web Service
Chemical structures database & machine learning with web services API
AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials. Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases. -
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DiSyIde
IDE for modeling and simulating discrete systems
...The application provides integration and a common control panel for DiSyMo (Discrete System Modeler) and DiSySi (Discrete System Simulator) applications, simplifying the workflow by providing a unified environment for modeling and simulation. This IDE provides a unified platform for both the graphical creation of system models (DiSyMo) and their dynamic simulation and control (DiSySi). DiSyMo enables users to intuitively design discrete system models using block diagrams, incorporating a wide range of elements such as adders, integrators, delay blocks, and other components. ... -
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LIGGGHTS
This is an academic adaptation of the LIGGGHTS software package
LIGGGHTS-PFM is a Discrete Element Method simulation package maintained for particulate flow modeling. It is based on the LIGGGHTS family and is intended for simulating granular materials, particles, powders, and bulk solids. The project supports Linux installation workflows and is often used alongside CFDEM-style coupling setups. It is useful for researchers and engineers studying particle mechanics, contact behavior, flow through equipment, and industrial bulk handling. The software... -
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ performs the preprocessing of Illumina next-generation sequencing reads (FASTQ files), making the workflow easier and more accessible than ever. Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf **Authors:** Milad Eidi Samaneh Abdolalizadeh Mohammad Hossein Nassirpour **Supervisors:** Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ, please cite the following preprint: **123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads** https://www.biorxiv.org/content/10.1101/2024.03.08.584032v1 **Important:** From now on, all future updates, releases, and related information for 123FASTQ will be made available through the project's GitHub page. ... -
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MathSteps
Step by step math solutions for everyone
mathsteps is a JavaScript library that performs step-by-step algebraic simplification and equation solving for expressions provided as strings. It exposes functions to simplify expressions and to solve equations, returning a structured sequence of steps that detail each transformation. For every step, mathsteps reports the original node, the change type, the resulting node, and any substeps, which makes it useful for education, debugging, and explainable math tooling. The library also... -
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Tiny Multi Bootloader+
Serial Bootloader for Microchip, Atmel, NXP, TI, 8051 microcontrolers
...This Bootloader consists of: - firmwares for many devices (this firmware need to be send to the device's flash memory with a programmer, only once) - a PC software which communicates with the bootloader firmware in the device and send the user's program in its memory Where does it come from? This Bootloader is based on "Tiny PIC Bootloader" made by Claudiu Chiculita. A special THANK to him!!! What can it do? It can program: - Microchip PIC10/12/16/18/24/32/dsPIC30/33 - Atmel ATtiny, ATmega - TI MPS430 - NXP ARM Cortex-M0+ - Silicon Labs C8051 And this: - with light modifications to the Bootloader firmware for new devices - without modifying your source code or using a special linker script - via GUI or command line prog - with automatic Reset -
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...More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.
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Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
Fusion gene detection by RNA-seq requires prior setup of several software modules and dependencies which might be troublesome. Furthermore, fusion detection tools tend to report many false positives. Therefore, we developed a detection and filtering workflow bundled into a Singularity container for a streamlined and easy-to-use application. Arriba and FusionCatcher are utilized for fusion calling. Our filtering pipeline uses read counts generated by FeatureCounts and insert size estimation by Picard Tools for calculation of our filtering metrics: Fusion Transcript Score (FTS). Further filtering is realized by a custom blacklist, our Promiscuity Score (PS) and Robustness Score (RS). ... -
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The Analyses Database is a collection of software to archive and to track rawdata files from analytical instruments. The system is set up using freely accessible tools - MySQL, apache, PHP, Linux. Several utilities for MS Windows are provided.
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PINCIS
PINCIS.pl is a Perl bioinf. script to analyze PICS data
...Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create). -
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ms
Tiny millisecond conversion utility
Use this package to easily convert various time formats to milliseconds. Works both in Node.js and in the browser. If a number is supplied to ms, a string with a unit is returned. If a string that contains the number is supplied, it returns it as a number (e.g.: it returns 100 for '100'). If you pass a string with a number and a valid unit, the number of equivalent milliseconds is returned. For added safety, we're using Template Literal Types (added in TypeScript 4.1). This ensures that you... -
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Data Logging Service
Process data logging service
...The Data Logging Service (DLS) is a data logging system for EtherLab, that is capable of collecting, compressing and storing high-frequency realtime data. The goal is, to allow the user unlimited and performant access to the stored data. A signal overview over a year is retrieved as fast as a tiny signal fluctuation, that happened in a fraction of a second. -
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Reproducible-research
A Reproducible Data Analysis Workflow with R Markdown, Git, Make, etc.
In this tutorial, we describe a workflow to ensure long-term reproducibility of R-based data analyses. The workflow leverages established tools and practices from software engineering. It combines the benefits of various open-source software tools including R Markdown, Git, Make, and Docker, whose interplay ensures seamless integration of version management, dynamic report generation conforming to various journal styles, and full cross-platform and long-term computational reproducibility. ... -
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AICtools
Workflow and set of tools for Automated Imagery Classification
AICtools is a GIS workflow and set of tools to facilitate Automated Imagery Classification (AIC) and analysis of surface features over time. Allows bulk processing of large data sets, including automated metadata processing/filtering, compressed archive extraction and file manipulation, raster band compositing, pre-processing, mosaicking, clipping. Automates a subset of operations involved in classification of satellite imagery and the associated raster calculations used for time trend analysis. -
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sciNote
Open source electronic lab notebook (ELN) for scientists
sciNote is an open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place. sciNote is specifically designed for life science students, researchers, lab technicians and group leaders. -
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MMAP
Multi-core Method for Analysis Pipelines
For more information, please see home page. -
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Artha is a handy thesaurus based on WordNet with distinct features like global hotkey look-up, passive desktop notifications, regular expression based search, etc.. Artha may be used as a free open-source replacement to the proprietary WordWeb Pro.
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Python4Proteomics Course
Python course for Proteomics analysis
Python course (in Spanish) for Proteomics analysis using basically Jupyter NoteBooks. For more information, you can have a look at the readme.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/p4p/code/ci/default/tree/readme.md -
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SNHD-UNIPHI
Universal Public Health Information
Universal Public Health Information - architecture to span the health care continuum including messaging, warehousing, and analysis, visualization and reporting. -
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Another simpler implementation for float only uses integer types, we should use -msoft-float first or we get complex result, so we need this with huge or tiny exponents float.
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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 of... -
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TARQUIN
MRS/NMR analysis software
Analysis software for MRS/NMR data. Allows processing and fitting to be performed in a fully automatic workflow. -
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AI learning
AiLearning, data analysis plus machine learning practice
...We are also exploring other categories of open source solutions and protocols. I hope you will understand this initiative, combine this initiative with your own interests, and do what you can. Everyone's tiny contributions, together, are the entire open source ecosystem. We are iBooker, a large open-source community, we-media, and online earning community, with a QQ group of more than 10,000 people and at least 10,000 subscribers. The number of Github Stars exceeds 60k, and it ranks in the top 100 of all Github organizations. The daily up of all its websites exceeds 4k, and the peak of Alexa ranking is 20k. ... -
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Linux TinyCad
Linux tiny CAD for educational purposes
Linux TinyCad, or LiniCad, is a tiny CAD used for educational purposes. It is written in Python/Tk and its goals are to be as programmatically easy and small as possible. -
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MOIRAI
Simple Scientific Workflow System for CAGE Analysis
...After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. ...
