BOW - Bioinformatics On Windows

  •        82

A group of tools run on Windows for Bioinformatics. Include ported tools from Linux (e.g. BWA, SAMTOOLS), and later original Windows applications.

http://bow.codeplex.com/

Tags
Implementation
License
Platform

   




Related Projects

bwa - Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

  •    C

Note: minimap2 has replaced BWA-MEM for PacBio and Nanopore read alignment. It retains all major BWA-MEM features, but is ~50 times as fast, more versatile, more accurate and produces better base-level alignment. BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

reflow - A language and runtime for distributed, incremental data processing in the cloud

  •    Go

Reflow is a system for incremental data processing in the cloud. Reflow enables scientists and engineers to compose existing tools (packaged in Docker images) using ordinary programming constructs. Reflow then evaluates these programs in a cloud environment, transparently parallelizing work and memoizing results. Reflow was created at GRAIL to manage our NGS (next generation sequencing) bioinformatics workloads on AWS, but has also been used for many other applications, including model training and ad-hoc data analyses. Reflow thus allows scientists and engineers to write straightforward programs and then have them transparently executed in a cloud environment. Programs are automatically parallelized and distributed across multiple machines, and redundant computations (even across runs and users) are eliminated by its memoization cache. Reflow evaluates its programs incrementally: whenever the input data or program changes, only those outputs that depend on the changed data or code are recomputed.

openedge - Extend cloud computing, data and service seamlessly to edge devices.

  •    Go

OpenEdge is an open edge computing framework that extends cloud computing, data and service seamlessly to edge devices. It can provide temporary offline, low-latency computing services, and include device connect, message routing, remote synchronization, function computing, video access pre-processing, AI inference, etc. The combination of OpenEdge and the Cloud Management Suite of BIE(Baidu IntelliEdge) will achieve cloud management and application distribution, enable applications running on edge devices and meet all kinds of edge computing scenario. About architecture design, OpenEdge takes modularization and containerization design mode. Based on the modular design pattern, OpenEdge splits the product to multiple modules, and make sure each one of them is a separate, independent module. In general, OpenEdge can fully meet the conscientious needs of users to deploy on demand. Besides, OpenEdge also takes containerization design mode to build images. Due to the cross-platform characteristics of docker to ensure the running environment of each operating system is consistent. In addition, OpenEdge also isolates and limits the resources of containers, and allocates the CPU, memory and other resources of each running instance accurately to improve the efficiency of resource utilization.

openQRM - Datacenter Management and Cloud Computing Platform

  •    Java

openQRM a web-based open source datacenter management and cloud computing platform that integrates flexibly with your existing datacenter components. openQRM supports the all major virtualization technologies. It automates provisioning, virtualization, storage and configuration management, and it takes care of high-availability. A self-service cloud portal with integrated billing system enables end-users to request new managed servers and application stacks on-demand.

OpenNebula - Data Center Management Solution

  •    C++

OpenNebula provides solution for building and managing virtualized enterprise data centers and cloud infrastructures to enable on-premise IaaS clouds. OpenNebula interoperability makes cloud an evolution by leveraging existing IT assets, protecting your investments, and avoiding vendor lock-in. penNebula was designed to address the requirements of business use cases from leading companies and across multiple industries, such as Hosting, Telecom, eGovernment, Utility Computing and lot more.


CloudStack - Infrastructure-as-a-Service (IaaS) software platform

  •    Java

CloudStack CE is an open source Infrastructure-as-a-Service (IaaS) software platform, which enables users to build, manage and deploy compute cloud environments.

nextflow - A DSL for data-driven computational pipelines

  •    Groovy

With the rise of big data, techniques to analyse and run experiments on large datasets are increasingly necessary. Parallelization and distributed computing are the best ways to tackle this kind of problem, but the tools commonly available to the bioinformatics community traditionally lack good support for these techniques, or provide a model that fits badly with the specific requirements in the bioinformatics domain and, most of the time, require the knowledge of complex tools or low-level APIs.

nats-server - High-Performance server for NATS, the cloud native messaging system.

  •    Go

NATS is a simple, secure and performant communications system for digital systems, services and devices. NATS is part of the Cloud Native Computing Foundation (CNCF). NATS has over 30 client language implementations, and its server can run on-premise, in the cloud, at the edge, and even on a Raspberry Pi. NATS can secure and simplify design and operation of modern distributed systems. If you are interested in contributing to NATS, read about our...

Isis2 Cloud Computing Library

  •    

Isis2 is a new option for cloud computing that can enable reliable, secure replication of data even in the highly elastic first-tier of the cloud.

StratoSphere - Cloud Computing Framework for Big Data Analytics

  •    Java

The Stratosphere System is an open-source cluster/cloud computing framework for Big Data analytics. It comprises of An extensible higher level language (Meteor) to quickly compose queries for common and recurring use cases, A parallel programming model (PACT, an extension of MapReduce) to run user-defined operations, An efficient massively parallel runtime (Nephele) for fault tolerant execution of acyclic data flows.

OpenStack - Software for building Private and Public Clouds

  •    Python

OpenStack is a cloud operating system that controls large pools of compute, storage, and networking resources throughout a datacenter, all managed through a dashboard that gives administrators control while empowering their users to provision resources through a web interface.

Dasein Cloud - Open Source Cloud Abstraction Library

  •    Java

Dasein Cloud (pronounced "da z-eye-n") is a Java-based cloud abstraction layer that enables programmers to build applications under a "write-once, run against any cloud" philosophy. It provides an abstract model under which most IaaS and some PaaS services can be modeled. Developers write applications to the Dasein Cloud model and it is then translated into the underlying cloud provider model.

FOSS-Cloud - Virtualization- and Cloud-Services

  •    PHP

The FOSS-Cloud is a Software, which enables you, to build your own Private or your Public-Cloud. The FOSS-Cloud environment (software and hardware) is an integrated and redundant server infrastructure to provide cloud-Services, Windows or Linux based SaaS, Terminal Server, Virtual Desktop Infrastructure (VDI) or virtual server-environmens. It makes virtual machines available, which can be accessed from internally as well as from the Internet.

.NET Bio

  •    DotNet

.Net Bio is a language-neutral bioinformatics toolkit built using the Microsoft 4.5 .NET Framework to help developers, researchers, and scientists.

BioSharp

  •    DotNet

BioSharp is a pure and test-driven .NET library for use in bioinformatics and related fields.

crossplane - An Open Source Multicloud Control Plane

  •    Go

Crossplane is an open source multicloud control plane. It introduces workload and resource abstractions on-top of existing managed services that enables a high degree of workload portability across cloud providers. A single crossplane enables the provisioning and full-lifecycle management of services and infrastructure across a wide range of providers, offerings, vendors, regions, and clusters. Crossplane offers a universal API for cloud computing, a workload scheduler, and a set of smart controllers that can automate work across clouds. Crossplane presents a declarative management style API that covers a wide range of portable abstractions including databases, message queues, buckets, data pipelines, serverless, clusters, and many more coming. It’s based on the declarative resource model of the popular Kubernetes project, and applies many of the lessons learned in container orchestration to multicloud workload and resource orchestration.

cloud-custodian - Rules engine for cloud security, cost optimization, and governance, DSL in yaml for policies to query, filter, and take actions on resources

  •    Python

Cloud Custodian is a rules engine for managing public cloud accounts and resources. It allows users to define policies to enable a well managed cloud infrastructure, that's both secure and cost optimized. It consolidates many of the adhoc scripts organizations have into a lightweight and flexible tool, with unified metrics and reporting. Custodian can be used to manage AWS, Azure, and GCP environments by ensuring real time compliance to security policies (like encryption and access requirements), tag policies, and cost management via garbage collection of unused resources and off-hours resource management.

Eucalyptus - Scalable cloud software for IT and DevOps

  •    Java

Eucalyptus is open source software for building Amazon Web Services-compatible private and hybrid clouds. The cloud software pools together compute, network, and storage resources within your IT environment to create on-demand, self-service private cloud resources.

gnatsd - High-Performance server for NATS, the cloud native messaging system.

  •    Go

NATS Server is a simple, high performance open source messaging system for cloud native applications, IoT messaging, and microservices architectures. It implements a highly scalable and elegant publish-subscribe (pub/sub) distribution model. The performant nature of NATS make it an ideal base for building modern, reliable, scalable cloud native distributed systems.

cloud-custodian - Rules engine for cloud security, cost optimization, and governance, DSL in yaml for policies to query, filter, and take actions on resources

  •    Python

Cloud Custodian is a rules engine for AWS fleet management. It allows users to define policies to enable a well managed cloud infrastructure, that's both secure and cost optimized. It consolidates many of the adhoc scripts organizations have into a lightweight and flexible tool, with unified metrics and reporting. Custodian can be used to manage AWS accounts by ensuring real time compliance to security policies (like encryption and access requirements), tag policies, and cost management via garbage collection of unused resources and off-hours resource management.