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Primeur weekly 2017-07-31

Focus

ECMWF at the heart of weather and climate modelling as global challenge of societal relevance with game changing prediction capability through exascale ...

NVIDIA hits the top 10 in the TOP500 and Green500 lists with multi-tasking GPUs - NVIDIA Vice President Ian Buck explains ...

Exascale supercomputing

Oak Ridge National Laboratory acquires D-Wave 2000Q Cloud services to accelerate hybrid computing applications ...

Crowd computing

Dark ecology project will use past weather radar data to trace bird migrations ...

Quantum computing

Tiny dancer atoms could prove a hit with quantum computer scientists ...

Qubitekk licenses ORNL single-photon source approach for quantum encryption ...

Ultracold molecules hold promise for quantum computing ...

University of Sydney and Microsoft forge global quantum computing partnership ...

Focus on Europe

Prof. Jan de Boer joins Board of Directors at Netherlands eScience Center ...

Hardware

Cray to expand storage portfolio through strategic transaction and partnership with Seagate ...

Stampede2 storms out of the Corral in support of U.S. scientists ...

Nick Nystrom appointed Interim Director of PSC ...

CSIRO has chosen Dell EMC to build a new scientific computing capability, kicking off a new generation of research ...

One Stop Systems named one of San Diego's fastest growing companies ...

Applications

High risk of unprecedented rainfall in the United Kingdom simulated by Met Office supercomputer ...

NIH awards $9.3 million for further development of PHENIX structural biology software ...

Inaugural Collaborative Science Call yields six proposals melding genomics and supercomputing ...

Stampede supercomputer skyrocketed science ...

IBM combines All-Flash and storage software optimized for Hortonworks ...

PPPL researchers perform first basic-physics simulation of the impact of recycled atoms on plasma turbulence ...

Catch of the day: A net full of trees ...

Liquid electrolyte contacts for advanced characterization of resistive switching memories ...

Catch of the day: A net full of trees


This is a Phylogenetic Toolset. Credit: Earlham Institute.
25 Jul 2017 Norwich - SPECTRE, a new open-source software package, simplifies the complex business of creating phylogenetic networks and trees. It has been written by bioinformaticians at the Earlham Institute.

Visual representations of datasets are valuable for analysing the interrelatedness of species and for presenting findings for publication. However, networks in particular demand complex bioinformatics that challenges software developers and evolutionary biologists alike.

Popular tools for visualising non-treelike evolution use algorithms and data structures to create networks. However, so far there is a lack of high-quality open source software making it harder to reuse and manipulate code for new tools and projects.

Now SPECTRE makes the source code of popular programs openly available, enabling researchers to adapt code to their own needs. Software developers can also use parts of the code as building blocks for creating new methods. Bioinformaticians can also run the tools in High Performance Computing environments.

"With SPECTRE, we hope to help speed up innovation by developers in phylogenetic methods and make it easy for biologists to visualise and analyse their datasets themselves", stated Sarah Bastkowski from the Earlham Institute.

The package makes it possible to identify and understand conflicts in data caused by events such as horizontal gene transfer and hybridisation.

"When I presented my work at conferences, delegates often told me how useful the algorithms and data structures I created could be if I was able to make them easily accessible. I decided to package them with methods that were already in use and make the source code openly available for the first time", stated Sarah Bastkowski.

During her PhD, Sarah Bastkowski had to create her own algorithms, data structures and file parsers for working with split networks. With SPECTRE, researchers and software developers no longer have to start from scratch, saving time and avoiding some of the challenges traditionally associated with creating phylogenetic networks and trees.

Mapleson used his industry background as a software developer to ensure the software provides easy-to-use building blocks for developers and a user-friendly interface for biologists.

Not only can users create networks and trees using the tools, but they can also view, manipulate and save them as high quality graphics for use in publications.

"The comprehensive library of algorithms, source code and programs in SPECTRE make it a valuable new resource for further new developments in the field, including by students", stated Professor Vincent Moulton from the School of Computing Sciences at the University of East Anglia.

"As people use the software, they will have their own ideas for how to improve it. These ideas can be incorporated into it, helping to ensure that the library will continue to grow and flourish", he stated.

Some of the tools use distances between objects of study to measure relationships and could therefore be used in a number of other fields. For example, to study the evolution of languages or patterns in geographical landscapes.

Source: Earlham Institute

Back to Table of contents

Primeur weekly 2017-07-31

Focus

ECMWF at the heart of weather and climate modelling as global challenge of societal relevance with game changing prediction capability through exascale ...

NVIDIA hits the top 10 in the TOP500 and Green500 lists with multi-tasking GPUs - NVIDIA Vice President Ian Buck explains ...

Exascale supercomputing

Oak Ridge National Laboratory acquires D-Wave 2000Q Cloud services to accelerate hybrid computing applications ...

Crowd computing

Dark ecology project will use past weather radar data to trace bird migrations ...

Quantum computing

Tiny dancer atoms could prove a hit with quantum computer scientists ...

Qubitekk licenses ORNL single-photon source approach for quantum encryption ...

Ultracold molecules hold promise for quantum computing ...

University of Sydney and Microsoft forge global quantum computing partnership ...

Focus on Europe

Prof. Jan de Boer joins Board of Directors at Netherlands eScience Center ...

Hardware

Cray to expand storage portfolio through strategic transaction and partnership with Seagate ...

Stampede2 storms out of the Corral in support of U.S. scientists ...

Nick Nystrom appointed Interim Director of PSC ...

CSIRO has chosen Dell EMC to build a new scientific computing capability, kicking off a new generation of research ...

One Stop Systems named one of San Diego's fastest growing companies ...

Applications

High risk of unprecedented rainfall in the United Kingdom simulated by Met Office supercomputer ...

NIH awards $9.3 million for further development of PHENIX structural biology software ...

Inaugural Collaborative Science Call yields six proposals melding genomics and supercomputing ...

Stampede supercomputer skyrocketed science ...

IBM combines All-Flash and storage software optimized for Hortonworks ...

PPPL researchers perform first basic-physics simulation of the impact of recycled atoms on plasma turbulence ...

Catch of the day: A net full of trees ...

Liquid electrolyte contacts for advanced characterization of resistive switching memories ...