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Archive by tag | bioinformatics

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23 Feb 2018 | 12:00 BST

TechBlog: Software quality tests yield best practices

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: Software quality tests yield best practices

Life science research increasingly runs on software. A good fraction, perhaps even most of it, is made by academics, for academics: Rough around the edges, perhaps, but effective — not to mention free. But, is it of high quality?  Read more

Tags:

  • Alexandros Stamatakis
  • bioinformatics
  • evolutionary biology
  • jeffrey perkel
  • phylogenetics
  • techblog
  • technology

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10 Nov 2017 | 12:00 BST

TechBlog: Timothée Poisot: Data science for the rest of us

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: Timothée Poisot: Data science for the rest of us

Timothée Poisot recently travelled to London for MozFest 2017, “The world’s leading festival for the open Internet movement.” There, the quantitative and computational ecologist at the University of Montréal in Canada ran a session entitled “Scientific computing for the terabyte-less.” Here, he tells Naturejobs why life science research needn’t necessarily follow the Big Data model.  Read more

Tags:

  • big data
  • bioinformatics
  • jeffrey perkel
  • techblog
  • technology
  • Timothee Poisot

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03 Nov 2017 | 12:00 BST

TechBlog: Bioconda promises to ease bioinformatics software installation woes

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: Bioconda promises to ease bioinformatics software installation woes

Bioinformatics is notoriously complicated, what with its arcane command-line interface, complex workflows, and massive datasets. For the uninitiated, simply installing the software can present a problem.  Read more

Tags:

  • Bioconda
  • bioinformatics
  • jeffrey perkel
  • Johannes Köster
  • techblog
  • technology

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20 Oct 2017 | 12:00 BST

TechBlog: Interactive figures address data reproducibility

Posted by Jeffrey Perkel | Categories: Blog, Technology

Juicebox.js

It’s no secret these days that researchers increasingly are focused on data reproducibility and transparency.  Read more

Tags:

  • bioinformatics
  • epigenetics
  • Erez Lieberman Aiden
  • jeffrey perkel
  • Juicebox
  • techblog
  • technology

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16 Oct 2017 | 12:00 BST

TechBlog: The nanopore toolbox

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: The nanopore toolbox

For this week’s Technology Feature, Michael Eisenstein wrote about the technology, applications, and challenges of nanopore DNA sequencing. In brief, the technology involves threading intact pieces of DNA through a tiny aperture in a membrane or other barrier, through which a current flows. As each base passes, it disrupts that current in a characteristic way, allowing the sequence to be determined.  Read more

Tags:

  • bioinformatics
  • jeffrey perkel
  • nanopore sequencing
  • Nicholas Loman
  • Oxford Nanopore Technologies
  • techblog
  • technology

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15 Sep 2017 | 12:00 BST

TechBlog: Jupyter powers bioinformatics, again

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: Jupyter powers bioinformatics, again

Bioinformatics isn’t easy for newbies. It’s typically done on the Linux command line, where users direct the computer using text-based instructions rather than clicking a mouse.  Read more

Tags:

  • bioinformatics
  • Galaxy
  • GenePattern Notebook
  • jeffrey perkel
  • Michael Reich
  • Project Jupyter
  • techblog
  • technology

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11 Sep 2017 | 19:00 BST

TechBlog: HiPiler simplifies chromatin structure analysis

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: HiPiler simplifies chromatin structure analysis

For my recent Toolbox on 3D genome visualization tools, Nils Gehlenborg at Harvard Medical School clued me into two interesting pieces of software. One, HiGlass,was included in my article; a related tool, HiPiler, was not. But that doesn’t mean it’s not worth talking about.  Read more

Tags:

  • bioinformatics
  • epigenetics
  • HiGlass
  • HiPiler
  • jeffrey perkel
  • Nils Gehlenborg
  • techblog
  • technology

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05 Sep 2017 | 17:00 BST

TechBlog: Mike Goodstadt: A circuitous route to bioinformatics

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: Mike Goodstadt: A circuitous route to bioinformatics

Most coders come to bioinformatics by one of two routes. They’re either biologists skilled in programming, or programmers with an interest in biology. Mike Goodstadt, the programmer behind the genome-visualization tool TADkit, took a different approach.  Read more

Tags:

  • bioinformatics
  • epigenetics
  • genomics
  • jeffrey perkel
  • Mike Goodstadt
  • TADkit
  • techblog
  • technology

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01 Aug 2017 | 18:52 BST

TechBlog: Jupyter Joins the Galaxy

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: Jupyter Joins the Galaxy

There’s a galaxy of tools in the Galaxy bioinformatics environment — 4,807 at last count. With them, researchers can do just about anything, computationally speaking. One thing they couldn’t do was work with their data programmatically. Now, thanks to a recent software update, that gap has been filled.  Read more

Tags:

  • bioinformatics
  • Galaxy
  • James Taylor
  • jeffrey perkel
  • programming
  • Project Jupyter
  • techblog
  • technology

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17 Jul 2017 | 16:00 BST

TechBlog: The sound of DNA

Posted by Jeffrey Perkel | Categories: Blog, Technology

TechBlog: The sound of DNA

With an alphabet comprising just four letters, DNA sequence isn’t much to look at. So, when sequence analysis tools want to highlight key elements, they typically do so using colour, font, or by overlaying other types of information. In the not-too-distant future, there may be another option: Audio.  Read more

Tags:

  • bioinformatics
  • DNA sonification
  • jeffrey perkel
  • techblog
  • technology

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Naturejobs is the world’s leading dedicated science jobs board. The Naturejobs blog aims to be the leading online resource for scientists in academia and industry who seek guidance in developing their careers. The blog delivers a mix of expert advice and personal stories to help readers review, set and achieve their career goals. We like to interact with our readers – we want to know what you want to know. Please share your thoughts in the comments section and get in touch if you have content suggestions. Pitches for guest posts are encouraged and should be emailed to the editor Jack Leeming at naturejobseditor [at] nature.com
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