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.

Melitta 1021-01 AromaFresh Reparatur

Zu Weihnachten 2018 haben wir eine Kaffeemaschine geschenkt bekommen. Es ist eine Melitta AromaFresh 1021-10 mit Mahlwerk, relativ einfach zu bedienen und mit nur ein paar Einstellungen. Wir waren zufrieden, bis das Mahlwerk nicht mehr lief. Das war nach ca. 3 Monaten. Da es sich bei nicht der Mühe gelohnt hätte die Garantie für diese 115 Euro-Maschine in Anspruch zu nehmen, habe ich die Maschine selber repariert.
Von oben kommt man an das Mahlwerk heran. Die Schrauben zum Öffnen liegen unter der Mahlgutkammer und zwei Schrauben sitzen von unten, im Kaffeefilterausschwenkbereich. Hier war aber alle okay. Die Kontakte für das Mahlwerk und für den Mahlgutkammersensor saßen fest.
Von unten kommt man an die Hauptplatine heran. Nur eine Sicherungsschraube benötigt eine leicht modifizierten Schraubenzieher. Die Platine ist gut verarbeitet und die verwendeten Komponenten sind nicht zu beanstanden. Auch ist die einseitige Leiterplatte gut verlötet und nachträglich noch lackiert. Die einzige mögliche Problematik, die ich sah, war die geringe Lötzinnmenge auf der Bahn zum Relais, das den Mahlwerkmotor steuert (siehe Bild).

Ich habe die Lötbahn mit 60/40-Lötzinn aufgefüllt und danach etwas mit Isopropanol gereinigt (siehe Bild).

Zur allgemeinen Freude funktioniert das Mahlwerk danach wieder. :)

Nachtrag: Der Nachwuchs hat sich nach der Reparatur darüber beschwert, daß die Kaffeemaschine einen hohen Pfeifton von sich gibt. Eine Kontrolle mit Spectroid hat ergeben, daß ich tatsächlich noch nicht am Tinitus leide, sondern die Maschine permanent mit 8625 Hz vor sich hin pfeift. Somit wird Tröte jetzt jedesmal zwischen den Brauvorgängen 100% vom Stromnetz entkoppelt. ;)

Renaming sequences in a FASTA file

I got the problem of double sequence names after downloading a collection of genes. Some alignment programs like MAFFT do not mind this but Clustal (ClustalX) and GeneDoc were complaining about none-unique sequence names.
The easiest way to circumvent this problem is to number the sequences in a FASTA file with multiple sequences. The instruction I found on the web for this just added the numbers to the end of the names. This works fine as long as the names are not too long as some programs do not handle the full length sequence names. Also Seqkit version 0.10.0 had problems with this. Therefore I wanted to have the numbers in the beginning of the sequence names and came up with the following AWK instructions:

gawk '/^>/ {name=$0; printf("%s_%s\n", ">"i++, substr($name,2));next;} { print $0;}' infile.fasta > outfile.fasta

Included into a Windows batch script the instruction looks like this:

gawk '/^>/ {name=$0; printf("%%s_%%s\n", ">"i++, substr($name,2));next;} { print $0;}' %infile% > %outfile%

This instructions use GAWK and PRINTF. GAWK and PRINTF are part of the GNU coreutils and can be found in the GnuWin32 package or installed through Cygwin.