Nanopype: a modular and scalable nanopore data processing pipeline

Building a scalable global data processing pipeline for large astronomical photometric datasets

Astronomical photometry is the science of measuring the flux of a celestial object. Since its introduction in the 1970s the CCD has been the principle method of measuring flux to calculate the apparent magnitude of an object. Each CCD image taken must go through a process of cleaning and calibration prior to its use. As the number of research telescopes increases the overall computing resources...

Scalable Modular Platform for Data-Intensive Applications

A pipeline for RNA-seq data processing and quality assessment

SUMMARY We present an R based pipeline, ArrayExpressHTS, for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data qualit...

MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation

SUMMARY Analysis of high throughput metabolomics experiments is a resource-intensive process that includes pre-processing, pre-treatment and post-processing at each level of experimental hierarchy. We developed an interactive user-friendly online software called Metabolite Data Analysis Tool (MetDAT) for mass spectrometry data. It offers a pipeline of tools for file handling, data pre-processin...

Scalable and Modular Scheduling

Scheduling a program (i.e. constructing a timetable for the execution of its operations) is one of the most powerful methods for automatic parallelization. A schedule gives a blueprint for constructing a synchronous program, suitable for an ASIC or VLIW processor. However, constructing a schedule entails solving a large linear program. Even if one accept the (experimental) fact that the Simplex...