Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    The sugar conspiracy

    19th June 2016

    A long but interesting read: The Sugar Conspiracy.

    Posted in Links, Misc, Science, Society | No Comments »

    How to: install Windows 7 on a recent laptop/PC from a bootable USB drive

    12th June 2016

    If you had ever seen the not-so-descriptive error message
    A required CD/DVD drive device driver is missing,
    then you have been trying to install Windows 7 (possibly using a bootable flash drive) on a recent laptop or desktop.

    There are two major obstacles for a somewhat-dated Windows 7 when it sees modern hardware:

    • USB 3.0
    • SSDs and newer disk drives in general

    Fortunately, both problems are easy to fix.
    Just follow the steps below; skip steps 1 and 2 if you already have a bootable Win7 flash drive.
    Read the rest of this entry »

    Posted in how-to | No Comments »

    TSW-friendly task and note management software

    5th June 2016

    A while ago I was looking for GTD/TSW-compatible android app.
    I ended up using Trello, Keep, and Calendar.

    But I always keep looking for new/improved tools, as right now I feel the best one does not exist…
    (If the best one can exist at all – requirements and conditions change all the time, so there is no fixed perfect immovable target.)

    I have been contemplating trying out the TSW methodology, but neither Keep nor Trello are quite there yet.
    I ended up using Evernote; after recent management changes and actually trying to become profitable it may as well last long enough.

    Everything was fine and calm until I have found workflowy yesterday.
    In essence, it is very similar to the text-file-based system that I have been using for at least half a year.

    Briefly, it is a web-based text editor on steroids, with possibly infinite nesting lists and seemingly full keyboard shortcuts control – no mouse needed.
    I recommend that you try the demo – it seems to be fully functional, and there is no need to sign up.

    This discovery made me read through pages and pages of this class of software tools.
    Here is a very brief summary of my findings: Read the rest of this entry »

    Posted in Links, Misc, Notepad, Software | No Comments »

    Practical comparison of NGS adapter trimming tools

    1st June 2016

    I used to work with sequencing providers who were giving me fairly clean data.
    It was already barcode-separated, and had no over-represented adapter sequences.
    The only thing I had to do was to (optionally) quality-trim the reads, and check for biological contamination.

    Recently, however, I have come across some real-world data, which not only had contamination in it, but also quite a noticeable percentage of adapters.
    I did a quick test of multiple tools to see if they fit my requirements:

    • should be easy/logical to use: no arcane/convoluted command lines or config files
    • should detect adapters automatically, either using its own database or a provided plain FASTA file
    • should be reasonably fast
    • must leave no adapter traces behind: I prefer aggressive trimming

    I have tried the following tools:

    • fastq-mcf from the ea-tools package
    • skewer
    • TrimmomaticPE
    • cutadapt: haven’t used it directly, but it is used by some of the compared tools
    • bbduk from BBMAP
    • autoadapt
    • TrimGalore!

    Read the rest of this entry »

    Posted in Bioinformatics | No Comments »

    Nobody wants higher-quality, complete bacterial genomes

    24th May 2016

    This is a piece of rant.

    Disclaimer

    The story, all names, characters, genomes and incidents portrayed in this blog post are fictitious.
    No identification with actual persons (living, dead or undead), places, companies, and processes is intended or should be inferred.
    No animals were harmed in the making of this blog post.

    Let’s try answering a question:

    why are there many incomplete/draft bacterial genomes, and much fewer complete genomes?

    Read the rest of this entry »

    Posted in Bioinformatics, Rant | 2 Comments »

    WD Red price per terabyte in Europe in May 2016

    18th May 2016

    Prices were collected on May 18th, 2016, from amazon.de

    Price per terabyte of WD Red HDDs

    Capacity, TB
    Price, EUR
    EUR/TB
    625242
    520841.6
    415839.5
    311638.(6)

    Posted in Comparison, Hardware | No Comments »

    Streptomyces morphogenesis regulation: overview presentation

    13th May 2016

    Note: this post is just a placeholder/draft, it will be extended later. But it can already be useful ;)
    Read the rest of this entry »

    Posted in Science | No Comments »