GPU-basecalling under MinKNOW

I had terrible problems getting GPU-basecalling running again after the update of MinKNOW in september 2022. After a downgrade von Xubunut 22.04 to 20.04, which didn't give the desired result, I reinstalled Xubuntu version 20.04 from scratch and slowly build up the system again while using following sources for the installation of the GPU-guppy-basecaller.

https://community.nanoporetech.com/docs/prepare/library_prep_protocols/experiment-companion-minknow/v/mke_1013_v1_revcl_11apr2016/installing-gpu-version-of-guppy-with-minknow-for-minion

https://gringer.gitlab.io/presentation-notes/2021/10/08/gpu-calling-in-minknow/

Kudos to where they belong. I'll try to re-collect my steps and post the result on another page.

Make XChange PDF Viewer the standard PDF reader in Linux

I like the speed and functionality of the Tracker XChange PDF Viewer version 2 and use it already for a long time under Windows. Unfortunately I couldn't find an equivalent PDV viewer for Linux that has the same capabilities, especially regarding marking of text and OCR.
To make the reader available as default in OpenSUSE with Xfce i put the file "XChange PDF Viewer.desktop" with the following  content into the folder "/home/user/.local/share/applications/".

[Desktop Entry]
Version=1.0
Type=Application
Name=XChange PDF Viewer
Comment=Project-Id-Version: @PACKAGE@\nReport-Msgid-Bugs-To: i18n@suse.de\nPOT-Creation-Date: 2015-10-01 14:51+0000\nPO-Revision-Date: 2005-11-08 12:26+8\nLast-Translator: Steve Beattie \nLanguage-Team: English\nLanguage: \nMIME-Version: 1.0\nContent-Type: text/plain; charset=UTF-8\nContent-Transfer-Encoding: 8bit\nPlural-Forms: nplurals=2; plural=n != 1;\n
Exec=wine "/windows/wd/Program Files/Tracker Software/PDF Viewer/PDFXCview.exe" Z:%F %F
Icon=/windows/wd/Program Files/Tracker Software/PDF Viewer/PDF-XChange-Viewer.png
Path=
Terminal=false
StartupNotify=false

Schaub-Lorenz bei Techmoan

In a recent video from Techmoan I saw a familiar logo on the PCB of an STC Executel. You can see the logo in the video here. In the upper left corner you can see the logo and the number "8413". After some brain storming and searching I found out that this logo belongs to Standard Elektrik Lorenz AG (SEL) who sold their consumer market products under the brand name "Schaub-Lorenz".

In the video Techmoan explains that the telephone was made by Standard Telephones and Cables (STC). Now I wonder if it was actually produced by SEL. STC and SEL were both part of International Telephone & Telegraph (ITT). Bye the way, Techmoan showed a Schaub-Lorenz logo already before in a video about a Hi-Fi system. You can see it here.

Update:
I found on Binary Dinosaurs a picture of the package for the Excecutal that has a label from SEL.

The original version is here.
And here is the address on the package.

Standard Elektrik Lorenz AG
Hohenzollernstr. 16
Entrance Wittelsbacherstrasse
7530 Pforzheim
West Germany

Why do you use "there is" with plural noun?

Ich bemerke immer wieder wenn ich YouTube-Videos schaue, daß ich mich daran störe wenn im Englischen "is" mit dem Plural verwendet wird. Irgendwie schlägt da der alte Oxford-English-Unterricht durch und machmal zeiht sich dann bei mir alles zusammen. Endlich habe ich eine einigermaßen befriedigende Antwort für dieses Phänomen gefunden. Hier bei Quora gibt Mark Jones eine gute Erklärung.
Zitat:
"I think there is one other reason you hear that in speech. The noun subject controls the verb for plurals and normally precedes it in the sentence. But the there is construction puts the verb before the noun subject, so what happens is the speaker has already spoken the verb before they realize it needs to be plural, and you get an incorrect agreement simply because their brain did not anticipate it in time.
There are no excuses like this in writing."
Danke

**** HoKAlign ****

*** A GUI under Windows for several free command line driven sequence alignment programs ***

 

 Currently supported alignment programs

• ClustalW (GUI: ClustalX 2)
• ClustalW2 (GUI: ClustalX 1)
• Muscle (versions 3.6 and 3.7)
• MAFFT (supported, the source for Cygwin is stored in the subfolder \scr - obsolete, now uses the Windows "All-in-one version")
• T-Coffee
• KAlign
• DiAlign
• Prank (GUI: Prankster)
• ProbCons
• Amap
• ProDA
• PCMA
• POA

What you need in addition

• obsolete - Cygwin (http://www.cygwin.com/ ) to run MAFFT
• Java (http://www.java.com/ ) to run ReadSeq
• ReadSeq is used for the conversion of the input files into the Fasta format and, if necessary, for the conversion of the output files into the MSF format. (not in use currently as ClustalW is used for the convert function)

GeneDoc (http://www.nrbsc.org/downloads/, March 2, 2007) to display the MSF output files. You can get the latest version 2.7.001 with the EXE-file form May 27, 2007 from here.

JalView (http://www.jalview.org/ ) to display the MSF output files

A file viewer or editor. Here is a short list of possibilities:

• EditPadClassic
• HiEditor
• Metapad
• Proton (german)
• Notepad++
• Notepad2
• more here

The folders

• \ contains the compiled script (HoKAlign.exe) and the hokalign.ini file. Please adjust this ini-file according to your systems settings
• \bin contains the executables (if possible compressed with UPX), and batch files
• \doc contains available documentations for the alignment programs
• \mat contains matrixes used by DiAlign
• \pix contains pictures and icons
• \scr contains the source for MAFFT under Cygwin
• \seq contains example sequence files

Internet sources for the programs used

• Autohotkey: http://www.autohotkey.com
• UPX: http://upx.sourceforge.net/
• ClustalW: ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ - ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/
• ClustalW2: ftp://ftp.ebi.ac.uk/pub/software/clustalw2
• MAFFT: http://align.bmr.kyushu-u.ac.jp/mafft/software/
• Muscle 3.6: http://www.drive5.com/muscle/download3.6.html
• Muscle 3.7: http://www.tcoffee.org/Packages/Binaries/windows/
• T-Coffee: http://www.tcoffee.org/Packages/Binaries/windows/
• KAlign: http://www.tcoffee.org/Packages/Binaries/windows/
• DiAlign-TX: http://www.tcoffee.org/Packages/Binaries/windows/
  Additional files from here.
• Prank: http://www.ebi.ac.uk/goldman-srv/prank/src/
• Probcons: http://www.tcoffee.org/Packages/Binaries/windows/
• Amap: http://www.tcoffee.org/Packages/Binaries/windows/
• ProDA: http://www.tcoffee.org/Packages/Binaries/windows/
• PCMA: http://www.tcoffee.org/Packages/Binaries/windows/
• POA: http://www.tcoffee.org/Packages/Binaries/windows/
• ReadSeq: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

How to install

• Unpack the files form the Zip file while keeping the folder structur. C:\Program Files\HoKAlign\ would be a good place.
• Create a shortcut to the file HoKAlign.exe. Your desktop would be a good place to place this shortcut.
• Java is necessary to run ReadSeq and ATV (Archaeopteryx). ReadSeq or ClustalX are used for all programs that can not read or write MSF files (e.g. Muscle). So you should have installed Java.
• If you want to use MAFFT you must have installed Cygwin. After that you have to install the MAFFT package, stored in the /scr subfolder, as described here.

Common known problems

• The conversion from the GCG MSF format into the FASTA format with the help of ClustalW or ReadSeq does not work because the MSF file has a wrong format.
  Check with the editor (The E-button) the input MSF file. The first line of an MSF file should only contain "PileUP" (without the quotes).
• Error messages, due to alpha stage. :)

To do

after

• Version 0.2 alpha
  • Feature: The conversion form MSF to FASTA overwrites existing FASTA files. Temporary sequence (FASTA, MSF) files should be used for all the processes.
  • Update: of MAFFT to the Cygwin free All-in-one package for Windows
  • Update: of Muscle to version 3.8
  • Error: The program can be started without a sequence file when "Cancle" is pressed during the startup dialoge. This is not intendet.
  • Error: The last produced tree file may not be opened due to different file endings (dnd, ph, phb)
  • Feature: Check of errorlevel outputs to give feedback on run problems.
  • Feature: Implementation of ProDa
  • Feature: Implementation of Gblocks for block masking
  • Feature: Implementation of Clustal Omega
  • Feature: "Tree only" option
  • Feature: Implementation of FastTree
  • Feature: User selection of conversion with ClustalW or ReadSeq

---

The program comes without any warrenties.
Benutzung auf eigene Verantwortung.
"As is" software.
You have to accept the copyrights of all included programs.
HoKAlign itself is freeware.

---

Download

Full package
Update to version 0.3.1

---

LAMP csv2tsv

Convert exported LAMP files from CSV to TSV for import into Excel

When working with LAMP (Loop-mediated isothermal amplification) data exported from the Eiken LA-500 machine I needed to import it into the none-American version of Excel. For this I wrote a little script to convert the CSV file into a TSV file.

@echo off
set infilename=%~n1
echo infilename ist: %infilename%
set infileext=%~x1

echo infileext ist: %infileext%
set infilefullpath=%~f1
echo infilefullpath ist: %infilefullpath%
set infilepath=%~p1
echo infilepath ist: %infilepath%
set infiledrive=%~d1
echo infiledrive ist: %infiledrive%

echo Looking for: %infiledrive%%infilepath%%infilename%.tsv.txt
if exist "%infiledrive%%infilepath%%infilename%.tsv.txt" goto file_exists
:: make working copy
copy %1 %tmp%\csv2tsv.tmp

:SED
:: replace in-place comma with tab
sed.exe -i "s/,/\t/g" %tmp%\csv2tsv.tmp
:: replace in-place full stop with comma
sed.exe -i "s/\./,/g" %tmp%\csv2tsv.tmp
:: copy final file to destination
copy %tmp%\csv2tsv.tmp "%infiledrive%%infilepath%%infilename%.tsv.txt"
:: cleanup tmp-file
del /Q %tmp%\csv2tsv.tmp
::
echo Done replacing commas with tabs and full stops with commas.
echo Enjoy your new tsv-file. :)
goto End

:file_exists
echo.
echo The file %infiledrive%%infilespath%%infilename%.tsv.txt allready exists! Aborting!
sleep 3
goto End

:End
echo.
echo The End!
sleep 1
::pause
goto :eof

Extended Nucleic Acid Sequence Massager

Long time ago I adjusted the Nucleic Acid Sequence Massager from Attotron to include some functions I needed. Base counting, MediaWiki formatting and reverse complementation were some off them. Here my link to a webpage I have set up so that everyone can use it. Enjoy.

Extended Nucleic Acid Sequence Massager

Please, also check out he other tools on my old BioTools page.