Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

Browsing Posts tagged SBW2014

One of the highlights of the Swedish Bioinformatics Workshop 2014 was of course the dinner entertainment, a song specially crafted for the event. It has now, fortunately, been put online. For anyone who might not catch all the words, here’s the complete lyrics for the song (which is based on the song “Java Jive” in the Manhattan Transfer arrangement):

The Bioinformatics ABC

Grab your coffee
Grab your tea
Put down your spoon now and listen to me
For the bioinformatics ABC
Wake up, wake up, wake up, wake up, wake up

And C for Clustal, though it’s not that fast
Alternatives are Muscle and MAFFT
ABYSS and BLAST and Clustal, Muscle, MAFFT

D count reads with DESeq or E for EdgeR
And F for FastQC and G for GLIMMER
H for HMMER using Markov Chains
Hidden hidden Markov model

I for Inchworm;
Add Chrysalis and Butterfly and wish
Assemble fast with a sound that goes swish
Contig, contig, contig, contig, transcript

And the ton of tools for metagenomics
MEGAN, Megraft,
MetaPhlan, MG-RAST, Meta-GeneMark
And that’s just mentioning a few of them
(Talk it boy)

N for Newbler, old-school it is
If you’re still using 454 it’s a bliss
O for Oases, P for PyroNoise

Q is for Quake for that great quality
And R is for all those neat statistics
S for the Spades assembler, oh yeah

T for TopHat
U for Uclust
V for Velvet

There is Wham to align
XMatchView to review
And YASS to pursue
(But do you)
Know any tools beginning with Z?
Yeah, Zorro, Zorro, Zorro
Oh yeah

I would like to sincerely apologize for that I have been terrible at responding to support issues pertaining to ITSx, Metaxa, Atosh etc. lately. I am currently on 50% parental leave and at the same time I am wrapping up three first-author papers, organizing a workshop and preparing a talk. Thus, support issues has been lagging a bit behind the last weeks to be able to cope with everything else. I have been ticking off most (all?) of my support questions the last couple of days, but if I have any remaining issues that I have missed to reply to, please re-send them to me!

I will try to improve response times, but it is hard when I am working less than usual (also, note that I (strangely) don’t get paid for supporting software, so I have to do this on my “sparetime”). My aim is to respond within a few days, so if I have not done so, please resend your e-mail with a friendly reminder that you are waiting for my response. Reminding me will very likely put your question up the priority pile.

So, my advice to becoming dads is: Do take paternal leave. Do take a lot of it. Share responsibilities with your partner. Because what you get back is awesome. (And also you get a good reason not to answer support questions in time.) But finally, don’t plan to wrap up the last couple of year’s worth of work and arrange a conference at the same time as you take out paternal leave. That will only make you feel insufficient at all fronts.

Keep the spirit high!

I would like to bring your attention to that the abstract deadline for the Swedish Bioinformatics Workshop held in Gothenburg in October has been extended to September 15. So hurry on and contribute with your latest research, we look forward to get to know what you’re doing!

I am part of the organizing committee for the Swedish Bioinformatics Workshop (#SBW2014) that will be held October 23-24 this year in Gothenburg. I would like to invite you all, especially master/PhD students and PostDocs in Sweden, to come and share the event with us!

SBW is an annual event that has been organized by the different universities in Sweden. This year it will take place at the Wallenberg Conference Centre in Gothenburg and is arranged by both University of Gothenburg and Chalmers University of Technology. SBW2014 will, as the tradition abides, be a meeting point for PhD students and postdocs working with any kind of bioinformatics within Sweden and is therefore free of charge for these groups. We are proud to announce a program including both invited speakers – such as Mick Watson from the Roslin institute, Dawn Field from University of Oxford, and Joakim Lundeberg from KTH – along with participant presentations and poster sessions. This year, the program will also contain a number of workshop sessions where hands-on problems will be used as starting points for discussions on new bioinformatics approaches to these problems. This will provide opportunities for attendees with different methodological backgrounds to interact and work together to find synergies between fields and come up with creative solutions.

More information about the event including registration and abstract submission can be found at www.sbw2014.se.

I, and the rest of the organizers, look forward to meeting you in Gothenburg in October!

Webpage: http://www.sbw2014.se

Facebook: https://www.facebook.com/events/1450513325188910/

Google+: https://plus.google.com/events/cuhlpovcc275stut854dk5ussnk

If you want, you can spread the word, for example using this flyer!