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Lab Notes

Lab Notes

Lab Notes

Whitepaper: Containerized Genomic Workflows with Singularity – Part 3

Author: Paolo Di Tommaso Deploy containers at scale with Nextflow Containers are exceptionally useful in scientific workflows. They allow for the encapsulation of software dependencies…

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Update to examples – November 9

Sylabs continues to provide example Singularity containers. Our latest installment of updates is as follows: ContikiOS Contiki is an open source operating system that…

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Whitepaper: Containerized Genomic Workflows with Singularity – Part 2

Authors: Gwendolyn Kurtzer, Keith Cunningham, Eduardo Arango Singularity Containers As mentioned in the first post “The quick uptake of nf-core amongst the bioinformatics community is…

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Update to examples – October 26

Here are a few more Singularity containers, that we at Sylabs have put together: Caffe Caffe is a Deep Learning framework. https://github.com/sylabs/examples/tree/master/machinelearning/caffe Singularity Definition…

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Whitepaper: Containerized Genomic Workflows with Singularity – Part 1

Authors: Phil Ewels, Sven Fillinger, Alex Peltzer, Paolo Di Tommaso Current Challenges with Genomic Pipelines Genomic workflows are becoming increasingly important in biomedical research, and also in everyday…

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Spark on Singularity

Apache Spark is a fast, in-memory data processing engine applicable to large-scale data processing, for both batch and streaming machine learning that requires fast…

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RStudio – IDE and Server powered by Singularity

RStudio is an Integrated Development Environment (IDE) for the R language. By containerizing RStudio, a scientist can leverage the reproducibility and portability of the…

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Jupyter Notebook containerized with Singularity

Jupyter Notebook containerized with Singularity Jupyter Notebook is an open source web application environment used to create and share documents containing code, equations, visualizations and…

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Facebook Research – Detectron and Singularity Containers

Detectron is an object detection system written in Python and powered by Caffe2. Detectron is a Facebook Research project created to solve real world…

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Containerizing Arnold Renderer with Singularity 3.0

Arnold is an advanced Monte Carlo ray tracing renderer built for the demands of feature-length animation and visual effects rendering, largely used to create…

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NodeJS on Singularity

We knode you would want NodeJS on Singularity so we you made a recipe. Setup: On your host, create a folder called “node” where we…

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Weka Data Mining with Singularity

Weka is a commonly used Machine Learning suite of algorithms for Data Mining with Java.  We’ve developed a Singularity container so that your Weka…

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New Containers – Apache, MariaDB, Blender

For 3.0, we’re developing containers for common use cases and expanding the size of our cloud library.  These containers and their recipe files will…

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Managing Singularity Branches

Greetings Singularity community! Based on a lengthy discussion about code organization during February’s hackathon, Singularity’s repository branches at https://github.com/singularityware/singularity will soon be reorganized. There…

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