Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

RNA sequencing (RNA-seq) experiments now span hundreds to thousands of samples. Current spliced alignment software is designed to analyze each sample separately. Consequently, no information is gained from analyzing multiple samples together, and it is difficult to reproduce the exact analysis without access to original computing resources. We describe Rail-RNA, a cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners. We use Rail-RNA to align 667 RNA-seq samples from the GEUVADIS project on Amazon Web Services in under 16 hours for US$0.91 per sample. Rail-RNA produces alignments and base-resolution bigWig coverage files, ready for use with downstream packages for reproducible statistical analysis. We identify expressed regions in the GEUVADIS samples and show that both annotated and unannotated (novel) expressed regions exhibit consistent patterns of variation across populations and with respect to known confounders. Rail-RNA is open-source software available at http://rail.bio.

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DEBKS: A Tool to Detect Differentially Expressed Circular RNA

10.1101/2020.10.14.336982 ◽

2020 ◽

Author(s):

Zelin Liu ◽

Huiru Ding ◽

Jianqi She ◽

Chunhua Chen ◽

Weiguang Zhang ◽

...

Keyword(s):

Open Source ◽

Rna Sequencing ◽

Open Source Software ◽

Simulated Data ◽

Circular Rna ◽

Host Gene ◽

Circular Rnas ◽

Biological Processes ◽

Rna Seq ◽

Disease Pathogenesis

AbstractCircular RNAs (circRNAs) are involved in various biological processes and in disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish between expression originating from BS and that from the host gene, we present DEBKS, a software program to streamline the discovery of differential BS between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

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Tibanna: software for scalable execution of portable pipelines on the cloud

10.1101/440974 ◽

2018 ◽

Cited By ~ 1

Author(s):

Soohyun Lee ◽

Jeremy Johnson ◽

Carl Vitzthum ◽

Koray Kırlı ◽

Burak H. Alver ◽

...

Keyword(s):

Web Services ◽

Open Source ◽

Open Source Software ◽

Source Code ◽

Software Tool ◽

Application Programming Interface ◽

Description Language ◽

Amazon Web Services ◽

Application Programming ◽

Programming Interface

AbstractSummaryWe introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network.AvailabilitySource code is available on GitHub at https://github.com/4dn-dcic/tibanna.

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IP Telephony Applicability in Cloud Computing

Journal of Science and Research Revista Ciencia e Investigación ◽

10.26910/issn.2528-8083vol3isscitt2017.2018pp128-133 ◽

2018 ◽

Vol 3 (CITT2017) ◽

pp. 128-133

Author(s):

Francisco Palacios ◽

Mitchell Vásquez Bermúdez ◽

Fausto Orozco ◽

Diana Espinoza Villón

Keyword(s):

Cloud Computing ◽

Web Services ◽

Open Source ◽

Open Source Software ◽

Ip Telephony ◽

Amazon Web Services ◽

Private Branch Exchange ◽

And Control

This paper carries out a research related to the applicability of VoIP over Cloud Computing to guarantee service stability and elasticity of the organizations. In this paper, Elastix is used as an open source software that allows the management and control of a Private Branch Exchange (PBX); and for developing, it is used the services given Amazon Web Services due to their leadership and experience in cloud computing providing security, scalability, backup service and feasibility for the users.

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Statistical analysis of popular open source software projects and their communities

2014 6th International Conference on Information Technology and Electrical Engineering (ICITEE) ◽

10.1109/iciteed.2014.7007913 ◽

2014 ◽

Author(s):

Andi Wahju Rahardjo Emanuel

Keyword(s):

Statistical Analysis ◽

Open Source ◽

Open Source Software ◽

Software Projects

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Data Analysis for Potential Reach Using Elasticsearch

Advances in Business Information Systems and Analytics - Exploring Enterprise Service Bus in the Service-Oriented Architecture Paradigm ◽

10.4018/978-1-5225-2157-0.ch012 ◽

2017 ◽

pp. 178-187

Author(s):

Nikhil Chaudhari

Keyword(s):

Data Analysis ◽

Web Services ◽

Open Source ◽

Real Time ◽

Service Oriented Architecture ◽

Online Activity ◽

Amazon Web Services ◽

Service Oriented ◽

Stream Analytics ◽

Real Time Application

Elasticsearch has become an attractive open-source search and analytics engine for use cases such as log analytics, click stream analytics and real-time application monitoring. As a service, Elasticsearch is made available by Amazon Web services, Searchly.com, Bonsai and many other websites as a hosted engine. This hosted Elasticsearch service is known as Elastic Cloud. The aim of AWS (Amazon Web Services) is to provide Elasticsearch as a service to users. These web services can implement Service-oriented Architecture. In the following chapter Potential Reach is aggregated using the server. Potential Reach is a metric that indicates the reach of an online activity like tweet or comment. This number helps media marketers track the success of the brand or company.

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The Statistical Analysis of Misreporting on Sensitive Survey Questions

Political Analysis ◽

10.1017/pan.2017.8 ◽

2017 ◽

Vol 25 (2) ◽

pp. 241-259 ◽

Cited By ~ 10

Author(s):

Gregory Eady

Keyword(s):

Statistical Analysis ◽

Open Source ◽

Open Source Software ◽

Multivariate Regression ◽

Large Scale ◽

Survey Question ◽

Direct Question ◽

Inherent Problem ◽

List Experiment ◽

The Right

What explains why some survey respondents answer truthfully to a sensitive survey question, while others do not? This question is central to our understanding of a wide variety of attitudes, beliefs, and behaviors, but has remained difficult to investigate empirically due to the inherent problem of distinguishing those who are telling the truth from those who are misreporting. This article proposes a solution to this problem. It develops a method to model, within a multivariate regression context, whether survey respondents provide one response to a sensitive item in a list experiment, but answer otherwise when asked to reveal that belief openly in response to a direct question. As an empirical application, the method is applied to an original large-scale list experiment to investigate whether those on the ideological left are more likely to misreport their responses to questions about prejudice than those on the right. The method is implemented for researchers as open-source software.

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