Balti and Bioinformatics

Balti and Bioinformatics: 28th September 2016

Balti and Bioinformatics returns …….

University of Birmingham 28th September 2016

How to get here

Location: Room WG04, Biosciences Building, University of Birmingham

(From University Station, turn left, walk down hill, Biosciences is 3 minutes walk and on your left. Walk in and follow the signs, we are on the ground floor).

Agenda

12.30 - Samosas and cha(a)t

1.30 - Science session

1.30 - tbc: Aaron Darling, iThree Institute, Sydney, Australia

2.00 - Doing bioinformatics: a user’s perspective: Lex Nederbragt, University of Oslo, Norway

2.30 - Tea and coffee

3.00 - Bioinformatics pipeline session

3.05 - Ansible versus Docker for packaging hard to run pipelines, Nick Loman, University of Birmingham

3.15 - Marius Bakke, University of Warwick, GUIX for Bioinformatics

3.25 - Shovill: The Spades Optimiser, Torsten Seemann, University of Melbourne

3.45 - Degust: RNA-Seq visualisation, David Powell, Monash

4.05 - Open discussion about pipelines

5.00 - Finish, taxis, balti at Dosa Mania, Harborne

Sign-up form here

Balti and Bioinformatics: 5th May 2015, Birmingham

Tuesday, 5th May 2015

WG04, Biosciences University of Birmingham B15 2TT

Building R27 on Campus Map: http://www.birmingham.ac.uk/Documents/university/edgbaston-campus-map.pdf

http://www.birmingham.ac.uk/contact/directions/getting-here-edgbaston.aspx

Suggest parking in North East car park (B15 2SA), 10 minutes walk from Biosciences.

For those arriving by train, the venue is a few minutes walk from University (Birmingham) train station which is 10 minutes from Birmingham New St. When buying your ticket, ensure that the destination is University (Birmingham).

13:00 - 16:30, then straight off for a curry.

“Revenge of the Commonwealth”

I’d quite like to bring this balti and bioinformatics meeting “back to basics”. The last few have got quite large, and talk- heavy, whereas I originally envisaged these meetings as a community forum for bioinformaticians to talk openly about problems they were encountering, and get the benefit of a diverse group of people struggling with their own problems. And hopefully to make strong connections that would outlast the meeting and lead to collaborations or self-help groups etc.

But we will have great talks too, and this is your opportunity to answer the question which is very much to the front of any British person’s mind, namely: which of the ex-colonies are managing better without us, Australia or Canada?

So I am going to limit the number and length of talks down a bit, and try and carve out some more structured and unstructured discussion time which would include “solve my problem” sessions and also just more discussion generally, and perhaps cap the numbers to something like 50.

Email me suggested topics.

The sign-up form is over heeeeeeeeeere.

Talks:

Jennifer Gardy, British Columbia Center for Disease Control (BC CDC) Using sequencing to determine if an outbreak is over.

Ana Crisan, BC CDC Visualizing heterogenous clinical and genomic data to support TB clinical teams

Jen Guthrie, BC CDC tbc

Torsten Seemann, University of Melbourne Snippy - rapid variant and core genome construction

Simon Gladman, University of Melbourne Microbial Genomics Virtual Laboratory

Nick Loman, Univeristy of Birmingham Update on CLIMB service

Balti and Bioinformatics On Air: 21st January 2015

The plan this year for the triumphant Balti and Bioinformatics series is to alternate between virtual, “on-air” meetings (where sadly you will need to provide your own balti curry) and real life ones which will be mainly held in Birmingham, but may be in other places in England or Wales. Ideally I would plan to run 6 meetings a year.

So … to kick us off:

Balti and Bioinformatics On-Air

This meeting’s theme is open data and reproducible bioinformatics.

Wednesday 21st January, 4pm GMT (=11am EST, =8am PST, 00:00 China)

20 minute talks each (interactive Q&A through Google Hangouts enabled)

Draft schedule:

+0m C. Titus Brown, UC Davis: Self-interest: can it be a strategy for convincing scientists to share pre-publication data in a useful way?

+30m Scott Edmunds, GigaScience: New models for open data publishing

+50m Jane Landolin, Pacific Biosciences: Open Pacific Biosciences data for model organisms

+70m Michael Barton, JGI: nucleotid.es for de novo assembly benchmarking and Docker

+90m Nick Loman, U. Birmingham: Nanopore data updates and the “poreathon”.

+100m Dave Lunt, University of Hull: ReproPhylo - Reproducible phylogenetics.

+110m Discussion (are we on the right track? Challenges? Containers and VMs - beneficial or the wrong direction?)

Balti and Bioinformatics "On Air" Wednesday September 10th 2014

Doing something a little bit different, our balti and bioinformatics meeting goes virtual this time, with a Google Hangout-on-Air, streaming live to YouTube!

Join us for a nanopore-themed programme which will be streamed from Google Hangouts to YouTube.

Draft schedule (subject to change)

Times are British Summer Time (GMT+1)

Start: 14:00 BST, 13:00 GMT, 09:00 Eastern Standard Time

14.00 - Intro
14.05 - Clive Brown, Nanopore sequencing
14.45 - Nick Loman, Early data from nanopore sequencing: bioinformatics opportunities and challenges
15.15 - Matt Loose, Streaming data solutions for nanopore
15.30 - Josh Quick, Nanopore sequencing in outbreaks
15.45 - Torsten Seemann, Awesome pipelines for microbial genomics
16.15 - Finish

Please note that some talks may not be recorded, so make sure you tune in live so as not to miss anything!

Go register at Google Plus.

Update 11th September:

This went great! Please check out the entire event on Youtube:

Balti and Bioinformatics: 27th May, 2014

We're back after a bit of a hiatus following last year's triumphant Beatles and Bioinformatics (available to watch on YouTube).

As usual this is a meeting organised by juniors, aimed at those toiling at the coal-face (but all ages welcome!) with a strong focus on methods and technologies and discussion. We go for a Birmingham balti (it's a curry) afterwards. What's not to like?

Tuesday, 27th May 12-5.
Mechanical Engineering Lecture Theatre G29 (Ground Floor)
Building Y3 on Campus Map
University of Birmingham, Edgbaston, Birmingham, B15 2TT. Book trains to "University (Birmingham)" and go via Birmingham New St.

Park in the new multi-storey North East car park.

Strictly capped at 100 people, please register early at this link.

The loose theme: "Emerging technologies". Details to emerge.

AGENDA

12:30 Registration

Part I: New Technologies

13:00 - 13:05 Introductions

13:05 - 13:35 Alan McNally, PI, Nottingham Trent University, "Parallel independent evolution of pathogenicity within the genus Yersinia"

https://www.youtube.com/watch?v=AhOWyfkdWzM

13:35 - 13:55 Zhemin Zhou, Post-doc, Achtman Group, Warwick University - "Hidden markov models for detection of recombination and Darwinian selection from whole-genome data"

13:55 - 14:35 Mark Pallen and Tom Connor, the MRC Cloud Infrastructure for Microbial Bioinformatics Consortium (Universities of Warwick, Birmingham, Cardiff and Swansea) - "Introducing CLIMB"

https://www.youtube.com/watch?v=fZhw5FMLUjM&feature=youtu.be

14:35 - 14:40 Yannick Wurm, Queen Mary University of London - "Lessons learnt from cloud computing"

https://www.youtube.com/watch?v=mmMQw2gIozI

2014 05-27 - Opinion: Computing for genomics sucks. from Yannick Wurm

Discussion: Cloud computing for genomics

15:00 Tea, coffee

Part II: Microbial Genomics

15:20 - 15:40 Elita Jauneikaite, PhD student, University of Southampton, "Analysis of Streptococcus pneumoniae whole-genomes from Singapore"

15:40 - 16:00 Lauren Cowley, PhD student, Public Health England, Title Food festival: attack of the aggs

16:00 - 16:20 Justin O'Grady, University of East Anglia, "Rapid diagnostics-by-sequencing of low-input DNA samples"

16:30 - 16:50 Phil Ashton, Public Health England, "Routine sequencing of Salmonella enterica for identification and molecular epidemiology"

Discussion: WGS - why isn't this routine yet?

17:15 close, taxis and curry

Beatles and Bioinformatics: Our best meeting yet

Wow, so last Wednesday we held the fourth instalment of our Balti and Bioinformatics series which was a brilliant success, attracting over 100 participants. The idea of this meeting is to bring those developing cutting-edge bioinformatics methods together with those who actually use them. Thanks to the generous sponsorship of the Centre for Genomic Research at the University of Liverpool and the Medical Research Council and the BBSRC we were able to change up a gear, inviting two incredible international speakers: Sébastien Boisvert and Daniel Huson. We were also able to afford a proper lunch for everyone - of course this was the traditional Liverpool dish 'scouse'.

One thing that gave the meeting a little extra edge was that we did a live 'webcast' for the very first time through YouTube's live events system. Apart from a few issues with the sound right at the beginning, this was a great success and the YouTube statistics told me that 461 playbacks were made during the broadcast. There was also a flurry of Twitter activity on the #BeatlesAndBioinformatics hashtag (see the Storify by Surya Saha here) and we even managed to take a question over Twitter.

The great thing about the YouTube live events is that it also saves a copy, and so we are able to record the event for posterity. I've had a few people ask about how to set up such a webcast themselves, we will try and write a short guide for the blog at some point.

A great meeting, I am incredibly grateful to our speakers: Séb, Daniel, Chris Quince, Susannah Salter, Sujai Kumar, Mike Cox, Rebecca Gladstone and Chris Hayman. I am also massively grateful to the team at Liverpool for helping to organise; Neil Hall, Christiane Hertz-Fowler and especially Lesley Parsons. Also thanks to Christina Bronowski and Ian Goodhead and the Free State Kitchen for help with the evening catering. And finally to Barbara Myers, Paul Loman and Josh Quick for organising the live video webcast.

Finally, we ended up in the Cavern Pub where we were entertained by the guitar antics of The Amazing Kappa.

Check out the webcast!

http://www.youtube.com/watch?v=tSul_qDwvN4

You can even jump directly to a talk, thanks to the tags that Sebastien Boisvert has put in.

13.00 – KEYNOTE: Sebastien Boisvert, Université Laval, Québec, Canada – “Ray and Ray Cloud Browser for Metagenomics” 5:46

13.50 – Chris Stewart, University of Northumbria at Newcastle – “Development of the Gut Microbiome in Preterm Infants at Risk of Necrotising Enterocolitis and Sepsis” 59:48

14.10 – Chris Quince, University of Glasgow – “CONCOCT: Clustering cONtigs on COverage and ComposiTion” 1:15:32

14.30 – Susannah Salter, Wellcome Trust Sanger Institute – “What’s lurking in your kits?”1:39:00

15.10 – KEYNOTE: Daniel Huson – Center for Bioinformatics, University of Tübingen – “Identifying Organisms from a Stream of DNA Sequences” 2:32:30

16.00 – Sujai Kumar, University of Oxford – “Blobology: exploring raw (meta)genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots”3:10:50

16.20 – Mike Cox, Imperial College – “Copy number correction in 16S analysis” 3:33:16

16.40 – Rebecca Gladstone, University of Southampton / Wellcome Trust Sanger Institute – “Managing hundreds and thousands of bacterial genome sequences” 3:48:30

Cream Teas and Bioinformatics: Meeting Report In Pictures and Slides

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Session 1

SeqMonk Talk, Simon Andrews, Babraham Institute

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Measuring DNA methylation - What could possibly go wrong? Felix Krueger, Babraham Institute

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Tracking pathogens through time and space - David Studholme, University of Exeter

[iframe src="http://docs.google.com/viewer?url=http%3A%2F%2Fpathogenomics.bham.ac.uk%2Fblog%2Fwp-content%2Fuploads%2Fstudholme-bioinformatics-balti-exeter-september-2013.pdf&embedded=true" width="800" height="600" style="border: none;"][/iframe]

Session 2

The Social Life of Ants, Yannick Wurm, Queen Mary University of London

[iframe src="http://www.slideshare.net/slideshow/embed_code/25977819" width="800" height="600" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"][/iframe]

BugBuilder - James Abbott, Imperial College

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Balti and Bioinformatics: Midlands Sequencing and Bioinformatics Meeting: Monday, 20th May 2013

It's that time again! Balti and bioinformatics will return .. on Monday, 20th May 2013. Not dissimilar to last time, we will feature complimentary samosas from Smethwick's finest sweet shop, and hopefully without the bit where about 40 people had to crowd into my office. Spaces will be limited, please register to attend via the Google web form (it's free!).

Programme:

West Midlands Bioinformatics & Sequencing Meeting: Balti and bioinformatics

Monday, 20th May 2013

Venue: Room 311, Geography Building, University of Birmingham (not Centre for Systems Biology, Haworth Building, University of Birminghamt

The Geography Building is adjacent to Biosciences (R26 on the campus map here)

If you are coming by car, please see the University travel website for details on car parking. The South Car Park is usually most convenient.

If you are coming by train, the Geography Building is a very short walk from the University (Birmingham) train station, which in turn is 2 stops from Birmingham New Street on the Redditch line.

12:30 Registration

13:00 Introduction

The Antipodean Invasion (Lamingtons not supplied)

13:10 "Torsten's toolkit: VAGUE, Prokka, Nesoni, VelvetOptimiser and more" - Torsten Seemann, Monash University / Victorian Bioinformatics Consortium, Australia

13:40 "Tutorials in the cloud: Microbial genomics using Galaxy" - Simon Gladman, CSIRO / Victorian Bioinformatics Consortium, Australia

14:10 "The genomics of footrot disease" - Dieter Bulach, Victorian Bioinformatics Consortium, Australia

14:20 Samosa break

14:40 "Doctorin' the TraDIS: Analysis of data derived from Transposon-directed insertion-site sequencing", Roy Chaudhuri, Centre for Genomic Research, University of Liverpool

15:10 "Infrastructure isn't just hardware: TGAC's tools supporting data-driven informatics" - Robert Davey, The Genome Analysis Center (TGAC), Norwich

15:40 "Norovirus genomics", Liz Batty, Nuffield Department of Medicine, University of Oxford

16:00 "Experiments with Nextera" - Jelena Sostare, University of Birmingham

16:10 Bioinformatics clinic

16:30 Discussion, depart for balti in taxis

Midlands Sequencing and Bioinformatics Meeting: First Meeting Tuesday, 11th December

Getting to the meeting

The meeting is in the Centre for Systems Biology, 3rd Floor Haworth Building, University of Birmingham. Full details on how to get here. Note you will need to ring the bell to gain entrance.

If you haven't made up your mind how to travel, I'd strongly suggest taking a train, the University has a campus railway station called "University (Birmingham)" and the Centre for Systems Biology is a 2 minute walk down-hill from there. The University station is 5 minutes from Birmingham New Street (take a train in the direction of Redditch, Hereford or Longbridge).

If you are coming by car, park in either the North or the South Car Park which are for visitors. It's pay and display but only a few pounds. Don't try to get onto campus as even if you get past security you will not likely find a space. Further details on parking and public transport here ...

Lunch won't be provided, but we'll have some snacks at half-time (authentic Birmingham samosas).

Going for a balti afterwards: we'll take taxis to the Balti Triangle and then back to New Street. We'll aim to be back in town by 8pm so that people can get trains. Those that can stay out later may want to get a drink at the German Market with us.

Introduction

I posted previously about setting up a regular, informal sequencing and bioinformatics meeting in the Midlands area (open to all-comers). Things are coming together nicely with about 30 people from other institutions expressing interest, and so I'm pleased to announce the date of the first meeting will be the afternoon of Tuesday, 11th December. We have some great guest speakers lined up already.

Please register for the meeting (the first one is free) via the Doodle poll. If you want to be notified about future meetings, or discuss how future meetings could work please sign up to the Google group.

The loose theme for this meeting is metagenomics and assembly (and metagenomics assembly).

Lastly, if you want to give a short talk at this meeting, please get in touch with me directly. The schedule is now full!

Agenda

Venue: Centre for Systems Biology, 3rd Floor, Haworth Building, University of Birmingham. How to get here.

12.45 Registration

13.00 Introduction (Nick Loman, Birmingham)

13.10 - 13.50 Sequence Analysis using Compressed Data Structures (Jared Simpson, Wellcome Trust Sanger Institute. Jared is the author of the ABySS and SGA assemblers.)

13.50 - 14.15 Metagenomics for Diagnosis of Bacterial Infection: Bioinformatics Challenges (Nick Loman, University of Birmingham)

14.15 - 14.30 The Population Structure and Genomic Architecture of S. aureus (Richard Everitt, University of Reading)

14.30 - 15.00 Refreshments

15.00 - 15.40 Compressive computing for next-generation sequencing data: making assembly fast, easy, and sensitive (C. Titus Brown, Michigan State University. Make sure to read his blog. Titus is responsible for an exciting new approach to genome assembly he calls 'digital normalization'.)

15.40 - 16.00 High-throughput microbial population genomics using cortex_var (Zamin Iqbal, University of Oxford)

16.00 - 16.10 Hardcore MiSeq Action: run optimisation, dealing with low-diversity samples and some tasty 16S recipes (Josh Quick, University of Birmingham. Josh was one of the systems integration engineers on the MiSeq before joining our group, and there's very little he doesn't know about this machine).

16.10 - 16.30 The bioinformatics clinic
Format: bring a single slide introducing a problem you would like to discuss with the audience.

16.30 Ends - all welcome to come for a Brummy balti with the speakers.

20.00 (very latest) Return to Birmingham New Street