Microbiology, Metagenomics and Bioinformatics

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

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I just wanted to notify anyone who might be interested in following my more personal reflections on my month in Wisconsin (and in Michigan over EDAR4) that I will be updating my Wisconsin Blog at this site (hopefully) regularly. The blog updates are not visible on the first page, so you will have to actively go to the Wisconsin Blog page by clicking in the upper right of the page.

I have made my yearly updates to the web site (changing pictures and adding the yearly summary), and I just want to take the opportunity to wish all my visitors a happy 2016! My little family has been sick (at least one of us) during most of the holidays, so we have had a very calm Christmas and a very calm New Year’s. Hope you have had more fun!

Vacation

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This week is the first of my long summer break, and I will be on vacation until mid-August. This means that I will only read mail sporadically, if at all. For very urgent issues, please give me a call or send me an sms, and I will attend to your message as soon as possible (this of course only applies to those of you who have my number in the first place).

For support questions, there are a few options:

  • For questions regarding Metaxa or Metaxa2, please add “METAXA” to the beginning of the subject line of the e-mail.
  • For questions regarding ITSx, please add “ITSX” to the beginning of the subject line.
  • For other support questions, please add “SUPPORT” to the beginning of the subject line.

This way I can easily assess which mails that are urgent to reply to. Don’t add “IMPORANT” or “URGENT” since that will just invoke the spam filter.

I wish you all a very very great summer!

After receiving a devastating amount of comment spam in the last couple of days, I have decided to close all commenting functionality, at least temporarily, on this site. If you want to discuss or comment on anything, please send me an e-mail. I would love to re-post your thoughts on the website! It’s sad that it has come down to this, but I never received as much comments as I did e-mails anyway. Thanks for your understanding, and let’s keep in touch over e-mail (or ResearchGate)!

We’re approaching Christmas, and this year I will try to spend lots of time with my family and less time at the computer. We’ll see how that goes, but all in all it means that I will most likely not respond promptly to e-mails until after New Year’s, maybe not until January 8 or 9. If, for example, you have asked a support question and have not received a response before January 12 2015, then please feel free to re-send your e-mail as I should then at least have replied that I cannot solve your issue quickly.

A further note for the future is that I will be on parental leave with my lovely nine-month-old during the entire spring, so answering e-mails will not be my highest priority, and might be neglected entirely in periods. I apologize for all kinds of inconveniences that this might cause, especially for Metaxa, ITSx and Megraft users.

Merry Christmas and a Happy New Year!



Sorry for not answering mail the last couple of days. My wife gave birth to this little adorable girl six days ago and we are now utilizing the Swedish rights to child-care days off work as much as we can. I will be back at work in April, and will until then only answer mail sporadically (i.e. when the baby is sleeping and I’m not). Thanks for your understanding, and sorry for having any ITSx or Metaxa support issues wait!

A new year has begun, and it brings with it a few updates on the website. I have added a summary of the year 2013 from my perspective, and (as you may recognize) updated my picture on the front page. Briefly, this year will bring lots of exciting stuff. Personally, I am quite excited to finally be able to share the new version of Metaxa – Metaxa2 – which will be released to the public late this Winter (or early Spring). Additionally, I look forward to wrap up some manuscript on metagenomics and antibiotic resistance, which I have been working with for more than 2.5 years now. Also, we look forward to some super-intersting technology developments in DNA sequencing, with PacBio finally finding proper usage scenarios, Nano-pore sequencing around the corner, and super-multiplexing on the Illumina instruments. We’re in for a treat with DNA sequencing in 2014!

A poor excuse…

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I feel very sorry that I have been a little bit unresponsive for the last couple of weeks. I have received several questions regarding the PETKit and ITSx that i have not yet got around to answer. I am very sorry for that inconvenience. The reason (not a good excuse, but still) is that I have been overloaded with grant applications. This will continue through the rest of september, so please be patient until October if I don’t reply e-mails. If you need a quick response, please state so very clearly, and I might be able to squeeze you in before the start of October. Otherwise, see you at the other end of the tunnel! Thanks for the understanding.

Server upgrades

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I’ve been informed by my web service provider that there will potentially be downtime of this site on the 13th of February (Wednesday this week), due to a server upgrade. I hope this will cause as little trouble as possible (both for you and for me).

You know the feeling when your assembler supports paired-end sequences, but your FASTQ quality filterer doesn’t care about what pairs that belong together? Meaning that you end up with a mess of sequences that you have to script together in some way. Gosh, that feeling is way too common. It is for situations like that I have put together the Paired-End ToolKit (PETKit), a collection of FASTQ/FASTA sequence handling programs written in Perl. Currently the toolkit contains three command-line tools that does sequence conversion, quality filtering, and ORF prediction, all adapted for paired-end sequences specifically. You can read more about the programs, which are released as open source software, on the PETKit page. At the moment they lack proper documentation, but running the software with the “–help” option should bring up a useful set of options for each tool. This is still considered beta-software, so any bug reports, and especially suggestions, are welcome.

Also, if you have an idea of another problem that is unsolved or badly executed for paired-end sequences, let me know, and I will see if I can implement it in PETKit.