Latest From Galaxy UK

Computational Biologist / Bioinformatician @ TSL

The Sainsbury Laboratory is looking for a dynamic, motivated individual to join an exciting bioinformatics team. The team provides bioinformatics infrastructure and capability to the laboratory as well as carrying out exciting research linked to the core TSL objectives.

Opportunities you could exploit in this role:

Work across important projects related to plant pathology
Develop your skills in infrastructure and/or analysis and/or software engineering
Extremely strong connections to the worldwide Galaxy community
Develop your own research stream
World-class scientific collaborators in the wet lab
Develop open science pipelines and practice

Responsibilities of this role:

In concert with a SysAdmin and HPC tech support team maintain accessibility and utility of a Galaxy instance
Develop and provide training courses inc Software Carpentry courses
Provide ad hoc advice and guidance on bioinformatics experimental design and execution
Carry out high throughput analysis on varied lab projects

Applicants should have a PhD, preferably in a bioinformatics related field, together with a background in computational biology, molecular biology, microbiology, plant biology or a related field. Experience with several of the following activities would be desirable: microarray analysis, high-throughput sequence analysis, gene prediction, proteomic analysis, population genetics, quantitative genetics, phylogenetic analysis, comparative genomics, SNP and CNV analysis, programming of object recognition and imaging software. Prior experience of the Galaxy bioinformatics platform would be an advantage.

Candidates would be advantaged by an understanding of high-throughput genomic analysis and familiarity with widely used genomic and proteomic databases and methods. Competence with bioinformatic scripting languages, particularly Python and/or Perl, is essential, as is experience handling data from the Illumina platform or other high throughput sequence systems. A desire to develop and implement new tools and methods is highly advantageous. As the post will include some training responsibilities, the candidate must have excellent communication and interpersonal skills.

For more information or to apply click here.

Bioinformatics Scientist @ Rothamsted Research

The Applied Bioinformatics Group of Rothamstead Research is looking for a Bioinformatics Scientist, to work closely with other scientists on data intensive research projects from crops, pathogens, insects or microbes. Rothamstead uses the Galaxy bioinformatics platform for delivery of data analysis resources and much of the work would be based around using or developing analytical and visualisation methods for use within Galaxy.

This work will encompass:

  • Analysis of NGS datasets from genome or transcriptome sequencing projects
  • Development of bioinformatics tools and workflows for Galaxy
  • Training other scientists in NGS analysis and bioinformatics best practises
  • Managing our communication with scientists through website, newsletter and other social media

The ideal candidate will have

  • Degree in Bioinformatics
  • Interest in data analysis, training, communication and tool development.
  • Experience in the analysis of large biological datasets
  • Excellent programming skills in Python, R or Java

For more info, visit http://rothamstead.ac.uk. Deadline is the 12th July, 2015, 5.30pm.

The Galactic Summer of ’15

Summer 2015 starts not only with wind and rain but also with 70 new publications involving Galaxy (check it out on the official Galaxy Project website). The “hot” months of the year are filled with exciting science and events.

Galactic Conferencing is going to happen in July

The Galaxy Community Conference 2015 hosted at The Sainsbury Laboratory in Norwich is approaching with huge steps. In less than two months time Galaxy users from all over the world will meet, mix, and mingle; present, listen to, discuss, and, hopefully, develop and implement new ideas. To achieve that GCC 2015 offers two training days (Training SunDay and Training Day on the 5th and 6th July, with Training SunDay already booked out!) and two integrated Hackathons for Galaxy Coders and Data Wranglers (e.g. Workflow Developers and Galaxy Users). The general meeting will take place on the 7th and 8th July. The early bird registration deadline has now passed but you can still register, so if you have not already done so, visit the official GCC 2015 website. It is also possible to submit late poster and even late oral abstracts!

What else is going on this summer?

There will be a number of events happening around GCC 2015 (for a reminder, have a look here.)

On the 18th June there will be another GalaxyAdmins meeting. Peter Briggs of the University of Manchester will speak on Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester. Furthermore, GalaxyAdmins will have an in-person meetup at GCC2015.

Introduction to Galaxy at Glasgow Polyomics, 8th-9th June

On the 8th and 9th June Glasgow Polyomics is hosting a two day introduction on using Galaxy for NGS applications. The workshop is held by Dave Clements of Johns Hopkins University, responsible for Galaxy Community Training and Outreach (including leading the organisation of the fantastic Galaxy Community Conference series). The workshop was already a quarter full after registration opened a couple of days ago, so be quick and register here if you’re interested. And you should be interested 😉

27th April 2015: GCC2015 registration opens

We are proud to announce that registration for GCC2015 has opened earlier this morning. If you plan to visit us in Norwich this summer (4th-8th July), please register here. In addition to the general meeting on 7th-8th July, we will have two training days (5th-6th July) and two hackathons (4th-5th July). Check out the programme here.

It is also not too late to submit a poster abstract if you have not already done so (http://gcc2015.tsl.ac.uk/abstracts/). The deadline is the 1st May.

UK-based Events around GCC2015

This year’s Galaxy Community Conference (GCC2015) held on 6-8th July (4th-8th July if you count in the Hackathons and Training Days) in Norwich is embedded into a number of related events going on in the UK and Ireland. Please find the list of events below (or on wiki.galaxyproject.org in a nice tabular format).

Web/Galaxy Developer at Glasgow Polyomics / University of Glasgow

Glasgow Polyomics / Uni Glasgow are looking for a web / Galaxy developer.

Job Purpose
To implement user-friendly high-quality web-based software for bioinformatics analysis of data generated at the Glasgow Polyomics Facility, in the areas of genomics, transcriptomics, proteomics and metabolomics, by combining and extending existing software and newly developed algorithms. To develop the Galaxy server for Glasgow Polyomics and the University. To interact in a collaborative and service capacity with users across the College as well as external academic and commercial partners to maximise the output of their datasets through implementation of novel analytical methods. To be involved in dissemination of that knowledge to staff and students through mentoring and training.

More information and link to application instructions can be found at http://www.gla.ac.uk/about/jobs/vacancies/, search for reference 010363.

Galaxy Community Conference 2015 Update

This year’s Galaxy Community Conference (GCC2015) will take place from 6-8 July in Norwich, UK.

The GCC is the Galaxy community’s annual gathering of users, developers, and administrators. Previous GCCs have drawn over 200 participants, and we expect that to happen again in 2015. GCC2015 is being hosted by The Sainsbury Laboratory in Norwich, UK, immediately before BOSC and ISMB/ECCB in Dublin.

GCC 2015 Events

The GCC2015 meeting will be held on 7-8 July.

GCC2015 comes with associated pre-conference events such as Hackathons and Training Days. This year an additional Training Day (Training SunDay) will be offered, as well as a novel kind of Hackathon from the Galaxy power-user’s perspective.

  • Code Hackathon, 4-5 July

    An intense two-day hands-on collaboration to develop working code that is useful to the Galaxy community. If you know how to code, and want to contribute to one of the most successful open source projects in the life sciences, then please consider attending. See the Code Hackathon home page for more.

  • Data Wrangling Hackathon, 4-5 July (new)

    An intense two-day hands-on collaboration to develop cutting edge analysis pipelines that are useful to the Galaxy community. If you know data analysis, we would love to have you here to help us beat back those seemingly unsurmountable analysis challenges. See the Data Wrangling Hackathon home page for more.

  • Training SunDay, 5 July (new)

    Something new for GCC2015 is Training SunDay, an additional day of training offered the day before its older sibling Training Day, and featuring a single track with the most in-demand topics. You can attend both Training Days, or just one. Training SunDay features these three topics:

    • Introduction to Galaxy
    • RNA-Seq Analysis with Galaxy
    • Visualisation of NGS Data

    These three topics are also offered on Monday, the 6th July. You can register for one or both Training Days.

  • Training (Mon)Day, 6 July

    The schedule for Training Day, Monday, 6 July is available. Training Day features five parallel tracks, each with three, two and a half hour workshops. There are topics on using Galaxy, interacting with it programmatically, and deploying, administering, and extending Galaxy. No matter what you do with Galaxy, there are workshops for you.

Early Registration Opens in March

Early registration (save heaps) will open this month. Early registration is very affordable and starts at less than £40 per day for students and postdocs. If you work in data-intensive life science research, then it is hard find a meeting more relevant than GCC2015. We look forward to seeing you there.

Abstract Submission is Now Open

Abstract submission for Oral and Poster Presentations at the 2015 Galaxy Community Conference (GCC2015) is now open.

Abstract submission for oral presentations closes 10 April, while poster submission closes 1 May. Poster authors will be notified of acceptance status within two weeks of submission, while oral presentation authors will be notified no later than 24 April. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

GigaScience Logo

We are pleased to announce that again in 2015, any oral or poster presentation will also be eligible for consideration for publication in the GigaScience “Galaxy: Data Intensive and Reproducible Research” series (first announced for GCC2013). GigaScience is pleased to offer a 15% discount on article publishing charges for accepted papers from GCC2015.

GCC2015 Sponsorships

BioTeam Logo

We are pleased to announce that BioTeam will again be a Gold Sponsor for this annual event. This is the third year in a row that BioTeam has been a GCC Gold Sponsor.

Call for Sponsors

The 2015 Galaxy Community Conference (GCC2015) is now accepting Sponsorships. Your organisation can play a prominent part in the Galaxy community by sponsoring GCC2015. Sponsorship is an excellent way to raise your organization’s visibility.

Several sponsorship levels are available, including two levels of premier sponsorships that include presentations. Premium sponsorships are limited, however, so you are encouraged to act soon.

Please let the organisers (gcc2015-org AT lists DOT galaxyproject DOT org) know if you are interested in helping make this event a success.

Content adapted from The March 2015 Galaxy News of the GalaxyProject.

GCC2015: Abstract submission open

The GCC2015 organising committee is pleased to announce that abstract submission for Oral and Poster Presentations at the 2015 Galaxy Community Conference (GCC2015) is now open.

Abstract submission for oral presentations closes 10 April, while poster submission closes 1 May. Poster authors will be notified of acceptance status within two weeks of submission, while oral presentation authors will be notified no later than 24 April. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

About GCC2015

GCC2015 is hosted by The Sainsbury Lab, in Norwich, United Kingdom, in July 2015. GCC has been expanded this year and will now offer two hackathons, two Training Days, and a two day conference. The GCC2015 Training Days cover 15 different topics spanning the full Galactic spectrum of topics.

Voting for GCC2015 Training Day is now open. Please vote.

Topic voting is open 19-30 of January! If you even considering attending GCC2015, then please take a few minutes to review the nominated topics and then vote.

Topics were nominated by the Galaxy Community and then normalized into the (hopefully) complementary, non-overlapping set of topics. Once voting closes conference organisers will line up instructors and then publish a schedule before registration opens.

Vote now