Open OnDemand: A web-based client portal for HPC centers

Hudak, David E.; Johnson, Douglas; Chalker, Alan; Nicklas, Jeremy; Franz, Eric; Dockendorf, Trey; McMichael, Brian

doi:10.21105/joss.00622

Cited by 76 publications

(22 citation statements)

References 2 publications

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“…All parameters and variables can be found in the accompanying R file ( Source code 1 ). Seurat was run in RStudio through a web-based portal on the GHPCC using Open OnDemand ( Hudak et al, 2018 ).…”

Section: Methodsmentioning

confidence: 99%

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

Lawson

Shin

et al. 2020

eLife

103

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The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.

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Section: Methodsmentioning

confidence: 99%

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

Lawson

Shin

et al. 2020

eLife

103

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“…Additionally we created another web application hosted by the OSC OnDemand [54] platform. This application has multiple functionalities including the query of Ensembl gene ID or a novel sequence against one selected flavor of our databases.…”

Section: Methodsmentioning

confidence: 99%

PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

Johnson

Franz

et al. 2019

GigaScience

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Background Long thought “relics” of evolution, not until recently have pseudogenes been of medical interest regarding regulation in cancer. Often, these regulatory roles are a direct by-product of their close sequence homology to protein-coding genes. Novel pseudogene-gene (PGG) functional associations can be identified through the integration of biomedical data, such as sequence homology, functional pathways, gene expression, pseudogene expression, and microRNA expression. However, not all of the information has been integrated, and almost all previous pseudogene studies relied on 1:1 pseudogene–parent gene relationships without leveraging other homologous genes/pseudogenes. Results We produce PGG families that expand beyond the current 1:1 paradigm. First, we construct expansive PGG databases by (i) CUDAlign graphics processing unit (GPU) accelerated local alignment of all pseudogenes to gene families (totaling 1.6 billion individual local alignments and >40,000 GPU hours) and (ii) BLAST-based assignment of pseudogenes to gene families. Second, we create an open-source web application (PseudoFuN [Pseudogene Functional Networks]) to search for integrative functional relationships of sequence homology, microRNA expression, gene expression, pseudogene expression, and gene ontology. We produce four “flavors” of CUDAlign-based databases (>462,000,000 PGG pairwise alignments and 133,770 PGG families) that can be queried and downloaded using PseudoFuN. These databases are consistent with previous 1:1 PGG annotation and also are much more powerful including millions of de novo PGG associations. For example, we find multiple known (e.g., miR-20a - PTEN - PTENP1 ) and novel (e.g., miR-375 - SOX15 - PPP4R1L ) microRNA-gene-pseudogene associations in prostate cancer. PseudoFuN provides a “one stop shop” for identifying and visualizing thousands of potential regulatory relationships related to pseudogenes in The Cancer Genome Atlas cancers. Conclusions Thousands of new PGG associations can be explored in the context of microRNA-gene-pseudogene co-expression and differential expression with a simple-to-use online tool by bioinformaticians and oncologists alike.

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“…Representatives from multiple HPC centers gave us the same feedback: “how do we run this at our center”? With this feedback, in 2015 we applied for and were granted an NSF award (SI2‐SSE) to develop Open OnDemand, 2 an open‐source version of OSC OnDemand that other HPC centers would be able to install. The SI2 project ran from July 9, 2015, to January 31, 2019.…”

Section: Project Timelinementioning

confidence: 99%

Open OnDemand: State of the platform, project, and the future

Chalker

Franz

Rodgers

et al. 2020

Concurrency and Computation

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High performance computing (HPC) has led to remarkable advances in science and engineering and has become an indispensable tool for research. Unfortunately, HPC use and adoption by many researchers is often hindered by the complex way these resources are accessed. Indeed, while the web has become the dominant access mechanism for remote computing services in virtually every computing area, HPC is a notable exception. Open OnDemand is an open source project negating this trend by providing web-based access to HPC resources (https://openondemand.org). This article describes the challenges to adoption and other lessons learned over the 3-year project that may be relevant to other science gateway projects. We end with a description of future plans the project team has during the Open OnDemand 2.0 project including specific developments in machine learning and GPU monitoring.

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Open OnDemand: A web-based client portal for HPC centers

Cited by 76 publications

References 2 publications

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers

Open OnDemand: State of the platform, project, and the future

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