3,478 Works

rCASC implementation in Laniakea: porting containerization-based-reproducibility to a cloud Galaxy on-demand platform

Luca Alessandrì, Pietro Mandreoli, Marco Antonio Tangaro, Marco Beccuti, Raffaele Calogero & Federico Zambelli
Integrating rCASC in Laniakea: rCASC, Cluster Analysis of Single Cells [Alessandri et al. BioRxiv], is part of the reproducible-bioinformatics.org project and provides single cell analysis functionalities within the reproducible rules described by Sandve et al. [PLoS Comp Biol. 2013]. Laniakea [Tangaro et al. BioRxiv Bioinformatics] provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. The...

Emerging infrastructure for Biodiversity Informatics

Paul Kersey
Presentation of the Kew Garden Collection and an outline of the challenges for life science research infrastructures in documenting and studying global plant and fungal diversity and its uses for humanity. Presented at the ELIXIR All Hands meeting 2019 in Lisbon, Portugal.

Translating laboratory finding into action: a hospital role in public health control cycle

ISZAID IDRIS, Siti Juliana Hussin, Iiffa Nabilah Shamsuddin & Madihah Alias
Background: A hospital is usually equipped with at least one clinical laboratory where specimen or sample obtained from patient being translated into information. Such information is very much crucial especially in controlling the spread of various diseases. The objective study is to describe the cases of communicable disease diagnosed through laboratory confirmation in Selayang Hospital from 1st January 2018 until 31st December 2018.

Methodology: This was retrospective cohort and hospital based study. All notified cases that...

An ontology for the DMP Common Standard Model

João Cardoso & José Borbinha
Data Management Plans (DMP) are documents that describe the techniques, methods and policies on how data is to be created, documented, accessed, preserved and disseminated throughout a project’s life cycle.

Most funding agencies now require that researchers submit a DMP with grant applications. Unfortunately the resulting DMP documents display a series of issues. Such as: a varying level of detail according to the expertise and meticulousness of its creators, or a lack of consistency due to...

Ignoring the optimal set of tissue-specific metabolic networks can bias the intepretation of data

Pablo Rodríguez-Mier, Nathalie Poupin, Laurent Le Cam & Fabien Jourdan
Tissue specific constraint-based modeling approachess have proven useful as automatic ways of extracting and analyzing metabolic networks that capture the different metabolic states of cells. These methods integrate different sources of information such as stoichiometry, transcriptomics or metabolomics data that constrain the space of possible metabolic networks. This process is usually done by searching for a metabolic network that minimizes an objective function measuring the discrepancy between the observed data and the model. However, current...

Single-cell RNA-seq of differentiating human induced pluripotent stem cells reveals dynamic genetic effects on gene expression

Davis J. McCarthy
Developments in stem cell biology enable the study of cell fate decisions in expression, ASE, and eQTL dynamics across pseudotime. (B) Summary of the identified cluster dynamics, (C) Exemplars of the dynamic gene expression and dynamic genetic effects clusters shown in A. Shaded regions indicate standard error (+/- 1 SEM). Pseudo-temporal ordering yields stage-specific eQTLs early human development that are impossible to study in vivo. We use human iPSCs from 125 donors, a pooled experimental...

Gentle and fast isolation of single cells for downstream single cell sequencing

Soohee Cho, Junyu Lin, Cher-Lynn Soh & Nandor Roczo
To obtain full-length cDNA coverage with minimal cell input, plate-based single cell sequencing is considered. A significantly overlooked step in the plate-based sequencing workflow includes the isolation of single cells. Although traditional cell sorters have been used for isolating single cells, the high pressure and lengthy sorting time may cause cell death or unwanted alterations in gene expression. In order to observe single cells near a physiologically-relevant state, the speed and pressure of single cell...

Genotype- free demultiplexing of singlecell-RNA-seq

Jon Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D. McKinnon, Sally Mortlock, Alice Pébay, Alex W. Hewitt, Anne Senabouth, Stacey Andersen, Nathan Palpant, Han Sheng Chiu, Grant W. Montgomery, Joseph Powell & Lachlan Coin
A variety of experimental and computational methods have been developed to demultiplex samples from pooled individuals in a single-cell RNA sequencing (scRNA-Seq) experiment which either require adding information (such as hashtag barcodes) or measuring information (such as genotypes) prior to pooling. We introduce scSplit which utilises genetic differences inferred from scRNA-Seq data alone to demultiplex pooled samples. scSplit also extracts a minimal set of high confidence presence/absence genotypes in each cluster which can be used...

Stability and host specificity of phages Zorp and Tanis for use in phage therapies

Andrew Kapinos, Lauren Remijas, Canela Torres, Samuel Wu, Malcolm Phung, Ryan Ngo, Krisanavane Reddi & Amanda Freise
Antibiotic-resistant bacteria are becoming increasingly difficult to treat. In the United States, at least 2 million people are diagnosed with an antibiotic-resistant infection yearly (CDC 2013). Bacteriophage therapy serves as an emerging solution for the treatment of bacterial infections, and understanding environmental conditions that affect bacteriophage stability is fundamental to developing effective phage treatments. Additionally, bacteriophages exhibit a varying degree of host range specificity that determines their utility for targeting specific bacterial hosts and their...

The impact of burned soil microbial community composition on environmental recovery and bioremediation

Cindy Lopez, Luisa Meneses, Diana Ramirez, Baowen Zhang, Christopher Dao, Keith Mitchell, Krisanavane Reddi & Amanda C. Freise
Wildfires have previously been shown to affect symbiotic relationships and dynamic feedback loops between plants and soil microbes thought to be crucial in the long-term stability of fire-adapted ecosystems. Understanding the microbial metabolic pathways involved in these feedback loops would provide information regarding potential methods to promote faster burned site recovery and bioremediation. The objective of this study is to observe how the Skirball Fire has impacted the community composition and metabolic pathways of the...

PHENO – The Woody plant BrAPI implementation

Bruno Costa, Daniel Faria, Inês Chaves, André Cordeiro, Mário J. Silva & Célia Miguel
PHENO (brapi.biodata.pt) is the endpoint of the Breeding API (BrAPI), implemented by Biodata.pt, the Portuguese node of ELIXIR, with a major focus on the woody plant domain. PHENO aims to provide access to plant genotypic and phenotypic datasets. Plant phenotyping and linking to genotyping data is paramount to modern plant breeding aiming at increasing plant production under a wide range of environmental conditions.
Access to phenotypic and genotypic datasets annotated using common standards contributes for data...

EC projects with ELIXIR Hub involvement

Hannah Hurst
A summary of European Commission H2020 and Innovative Medicines Initiative (IMI) projects with ELIXIR Hub involvement.

These projects have received funding from the European Union’s Horizon 2020 research and innovation programme.

ELIXIR tools platform: software best practices

Mateusz Kuzak, Jennifer Harrow, Allegra Via & Fotis Psomopoulos
ELIXIR is an intergovernmental organization that brings together life science resources across Europe. These resources include databases, software tools, training materials, cloud storage, and supercomputers. One of the goals of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. ELIXIR's activities are divided into the following five areas Data, Tools, Interoperability, Compute...

Proof-of-concept implementation of human genomics variant calling pipeline using BioContainers and Galaxy

Giacomo Tartari, Salvador Capella Gutierrez, Castrense Savojardo, Pier Luigi Martelli & Rita Casadio
We present a proof-of-concept workflow from Laurie et al 2016, based on BioContainers and Galaxy. It includes one aligner, one BAM processor and one variant caller.
More specifically: Burrows Wheeler Aligner (BWA) is used to map NGS reads on the reference genome, the samtools and bcftools packages to process the BAM files and call variants, respectively. The tools, installed from the main Galaxy toolshed, were configured manually with Biocontainers images.

Containerized workflows provides a prominent advantage: the...

Setting up a Galaxy platform in a HPC infrastructure for genomics implementation into diagnosis routines for a health reference center

Miguel Juliá, Sara Monzón Fernández, Luis Chapado, Angel Zaballos & Isabel Cuesta
The Health Institute Carlos III (ISCIII) is the main Public Research Entity funding, managing and carrying out biomedical research in Spain. From its Bioinformatics Unit (BU-ISCIII), we give support to a great variety of research groups with different needs and expertise, and also external researchers from universities and public hospitals and their associated research centers. In order to provide a unified and user friendly platform to execute standard genomics analysis, use our in-house tools and...

Life cycle decisions in Mycobacteriophage MPhalcon

Alec Griffith, Raveena Mann, Riley Spurling, Andrew Lund, Krisanavane Reddi, Jordan Moberg Parker & Amanda Freise
Bacteriophages are the most abundant organism in the biosphere and are influential in soil ecosystems, affecting many biogeochemical cycles. Through horizontal gene transfer, temperate bacteriophages, which replicate via lytic or lysogenic life cycles, exchange genomic information with hosts. This affects bacteria-phage coevolution, genetic diversity, and microbial community structure. This study explored the conditions and parameters that influence lytic-lysogenic life cycle decisions of temperate mycobacteriophages, such as incubation at increasing temperatures and exposure to ultraviolet radiation,...

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