Category Archives: Software

Software

Transdermal vitamin D patch

There is a new clinical trial D3ForMe that has a big benefit in my eyes: Avoiding the high local vitamin D in the gut Peyers’ Patch after oral supplementation.
Oral supplementation likely affects gut-specific homing leading activated T cells and antibody-secreting cells (ASCs) to both inflamed and non-inflamed regions of the gut. Also antigen recognition may be affected by inhibited DC maturation.
In an earlier vitamin D3 could be safely be delivered through the dermal route.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

Wahlen mit alphabetischer Reihenfolge

Es gibt in Deutschland immer noch viele Kammer-, Sozial- und Vorstandswahlen, die aus angeblichen Fairnessgründen die Kandidatenliste alphabetisch reihen. Dabei wissen die meisten Organisationen nicht, wie sie sich damit vor allem selbst, aber auch den Kandidaten schaden.

Wahlen von Kandidatenlisten in alphabetischer Reihenfolge sind nämlich vor allem dann ein Problem, wenn A. die Wähler die Kandidaten nicht kennen, es B. einen großen Überhang von Kandidaten im Verhältnis zu den Gewählten gibt, C. die Reihung als Empfehlung missverstanden wird und D. die Wahlergebnisse relativ nahe beieinander liegen.

In der englischen Literatur ist das alles als “Ballot Order Effect” bekannt und kann auf vielen Blogs nachgelesen werden:
https://daily.jstor.org/ballot-position/
https://www.pulj.org/the-roundtable/avoiding-election-bias
https://www.bbc.com/news/blogs-magazine-monitor-27426319
https://www.cbc.ca/news/politics/grenier-ballot-order-1.4608059
http://www.centerforpolitics.org/newslet_909cb.html

Der Effekt ist enorm, mit einem Buchstaben im vorderen Drittel liegt die Wahlchance bei ca 65%, im mittleren Drittel bei 25%, im letzten Drittel bei 10%. Am Ende der Liste zu stehen ist besonders schlecht, auch bekannt als “voter fatigue” (das ändert sich allerdings wenn die Liste sehr lange ist, dann wird man wieder etwas häufiger gewählt).

Das folgende Beispiel illustriert an einem praktischen Beispiel, wie eine Liste von 20 Kandidaten am besten unter den Wählern verteilt wird, um den “Ballot Order Effect” zu vermeiden.

l <- LETTERS[1:20]
l
[1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" "Q" "R" "S" "T"

# Zuerst wird die alphabetische Reihenfolge aufgelöst
l <- sample(l)
l
[1] "Q" "C" "K" "F" "L" "M" "J" "T" "B" "I" "G" "H" "O" "P" "N" "S" "R" "A" "E" "D"

# Dann wird der jeweils letzte Namen nach vorne gerückt
r &lt;- NULL
for (v in l[20:1]) {
  x <- c( l[grep(v,l):20], l[1:(grep(v,l)-1)] )[1:20]
  r <- rbind (r,x)
}
r

# Jede Zeile gibt nun einen von 20 Wahlvorschlägen aus
  [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16] [,17] [,18] [,19] [,20]
x "D"  "Q"  "C"  "K"  "F"  "L"  "M"  "J"  "T"  "B"   "I"   "G"   "H"   "O"   "P"   "N"   "S"   "R"   "A"   "E"  
x "E"  "D"  "Q"  "C"  "K"  "F"  "L"  "M"  "J"  "T"   "B"   "I"   "G"   "H"   "O"   "P"   "N"   "S"   "R"   "A"  
x "A"  "E"  "D"  "Q"  "C"  "K"  "F"  "L"  "M"  "J"   "T"   "B"   "I"   "G"   "H"   "O"   "P"   "N"   "S"   "R"  
x "R"  "A"  "E"  "D"  "Q"  "C"  "K"  "F"  "L"  "M"   "J"   "T"   "B"   "I"   "G"   "H"   "O"   "P"   "N"   "S"  
x "S"  "R"  "A"  "E"  "D"  "Q"  "C"  "K"  "F"  "L"   "M"   "J"   "T"   "B"   "I"   "G"   "H"   "O"   "P"   "N"  
x "N"  "S"  "R"  "A"  "E"  "D"  "Q"  "C"  "K"  "F"   "L"   "M"   "J"   "T"   "B"   "I"   "G"   "H"   "O"   "P"  
x "P"  "N"  "S"  "R"  "A"  "E"  "D"  "Q"  "C"  "K"   "F"   "L"   "M"   "J"   "T"   "B"   "I"   "G"   "H"   "O"  
x "O"  "P"  "N"  "S"  "R"  "A"  "E"  "D"  "Q"  "C"   "K"   "F"   "L"   "M"   "J"   "T"   "B"   "I"   "G"   "H"  
x "H"  "O"  "P"  "N"  "S"  "R"  "A"  "E"  "D"  "Q"   "C"   "K"   "F"   "L"   "M"   "J"   "T"   "B"   "I"   "G"  
x "G"  "H"  "O"  "P"  "N"  "S"  "R"  "A"  "E"  "D"   "Q"   "C"   "K"   "F"   "L"   "M"   "J"   "T"   "B"   "I"  
x "I"  "G"  "H"  "O"  "P"  "N"  "S"  "R"  "A"  "E"   "D"   "Q"   "C"   "K"   "F"   "L"   "M"   "J"   "T"   "B"  
x "B"  "I"  "G"  "H"  "O"  "P"  "N"  "S"  "R"  "A"   "E"   "D"   "Q"   "C"   "K"   "F"   "L"   "M"   "J"   "T"  
x "T"  "B"  "I"  "G"  "H"  "O"  "P"  "N"  "S"  "R"   "A"   "E"   "D"   "Q"   "C"   "K"   "F"   "L"   "M"   "J"  
x "J"  "T"  "B"  "I"  "G"  "H"  "O"  "P"  "N"  "S"   "R"   "A"   "E"   "D"   "Q"   "C"   "K"   "F"   "L"   "M"  
x "M"  "J"  "T"  "B"  "I"  "G"  "H"  "O"  "P"  "N"   "S"   "R"   "A"   "E"   "D"   "Q"   "C"   "K"   "F"   "L"  
x "L"  "M"  "J"  "T"  "B"  "I"  "G"  "H"  "O"  "P"   "N"   "S"   "R"   "A"   "E"   "D"   "Q"   "C"   "K"   "F"  
x "F"  "L"  "M"  "J"  "T"  "B"  "I"  "G"  "H"  "O"   "P"   "N"   "S"   "R"   "A"   "E"   "D"   "Q"   "C"   "K"  
x "K"  "F"  "L"  "M"  "J"  "T"  "B"  "I"  "G"  "H"   "O"   "P"   "N"   "S"   "R"   "A"   "E"   "D"   "Q"   "C"  
x "C"  "K"  "F"  "L"  "M"  "J"  "T"  "B"  "I"  "G"   "H"   "O"   "P"   "N"   "S"   "R"   "A"   "E"   "D"   "Q"  
x "Q"  "C"  "K"  "F"  "L"  "M"  "J"  "T"  "B"  "I"   "G"   "H"   "O"   "P"   "N"   "S"   "R"   "A"   "E"   "D"    
# Diese 20 Wahlvorschläge werden nun in gleicher Stückzahl ausgedruckt und verteilt

# Bei online Wahlen lässt man einen Counter mitlaufen oder noch einfacher, man wirft
# alle 3 Sekunden den nächsten Vorschlag aus
r[ floor(as.numeric(format(Sys.time(), "%S"))/3), ]
[1] "J" "T" "B" "I" "G" "H" "O" "P" "N" "S" "R" "A" "E" "D" "Q" "C" "K" "F" "L" "M"

Es sollte also nicht all zu schwer sein, faire Wahlen durchzuführen.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Philosophy, Software

Depressed Former Internet Optimist

technology review explains a new breed

all this has given rise to a new breed: the Depressed Former Internet Optimist (DFIO). Everything from public apologies by figures in the technology industry to informal chatter in conference hallways suggests it’s become very hard to find an internet Optimist in the old, classic vein. There are now only Optimists-in-retreat, Optimists-in-doubt, or Optimists-hedging-their-bets.

and continues

Many Optimists believed that the structure of the internet by itself—manifested in collaborative projects such as wikis or crowdfunding—would bend social outcomes in their favor. One response to the events of 2016 has been to revisit this assumption, claiming that while the basics might have been right, more work is needed to realize the original vision.

So may I add here an advertisement of Tim Berner-Lee’s Solid project operating Inrupt?

Imagine if all your current apps talked to each other, collaborating and conceiving ways to enrich and streamline your personal life and business objectives? That’s the kind of innovation, intelligence and creativity Solid apps will generate.

As we are now redefining content why not also getting paid by Brave when browsing? The not not evil Alphabet company has already announced some major changes.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Philosophy, Software

On the irrelevance of hypothesis testing in the computer age

Geoffrey R. Loftus in Behavior Research Methods, Instruments, & Computers 1993, 25 (2), 25() 256

Hypothesis testing, while by far the most common statistical technique for generating conclusions from data, is nonetheless not very informative. It emphasizes a banal and confusing question (“Is it true that some set of population means are not all identical to one another?”) whose answer is, in a mathematical sense, almost inevitably known (“No”). Hypothesis testing, as it is customarily implemented, ignores two issues that are generally much more interesting, important, and relevant: What is thepattern of population means over conditions, and what are the magnitudes of various variability measures (e.g., standard errors of the mean, estimates of population standard deviations)?

so auch in G. Lind “Effektstärken: Statistische, praktische und theoretische Bedeutsamkeit empirischer Befunde”, Privatdruck 2012

Was aber selten (viel zu selten!) in Erwägung gezogen wird, ist die Möglichkeit, Befunde auf ihre theoretische, inhaltliche Bedeut- samkeit hin zu untersuchen: Welche Wertedifferenz ist für unser subjektives Empfinden und unsere Handlungen bedeutsam? Ab welcher Effektstärke können wir davon sprechen, dass eine Therapie- methode oder eine pädagogische Intervention wirklich etwas bringen und den Aufwand lohnen, den alle Beteiligten investieren müssen? Tritt der Effekt immer oder nur unter bestimmten Bedingungen auf? Ist er an Besonderheiten der Studie (Umfang des Samples, Streuung der unabhängigen Variablen) gebunden? Passt der Effekt zu dem, was wir bereits über die Variablen wissen, die wir untersuchen, oder stellt er fundiert geglaubte Theorien in Frage?

 

CC-BY-NC Science Surf , accessed 29.04.2026
Genetics, Software

New insights by single-cell genomics

Congress report Annual AGD Meeting 2018, Potsdam Oct. 5–6

Welcome and Opening of Symposium by  Peter Nürnberg, President of the AGD and Joachim L. Schultze, Chair of the Program Committee.

Joachim L. Schultze
Peter Nürnberg

The AGD meeting was interesting and a great primer for all of us who are not directly working with single cells.

Maybe it is an unusual research field – dissecting single cells in the first stage is not a trivial task. And single cell  means single cell experiment that can be replicated only in other cells. The current readout is  RNA content at a given time while genomics and proteomics still need to be integrated. Experiments cover mainly abundant RNAs and for cost reasons only the 3′ ends. The statistical analysis usually is a 2 dimensional PCA (known to overfit noise) so this not a trivial approach at all. Newly identified cell cluster need careful confirmation as addressed in the talk of Andreas Schlitzer.

Continue reading New insights by single-cell genomics →

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

If privacy is outlawed, only outlaws will have privacy

http://www.philzimmermann.com/EN/essays/WhyIWrotePGP.html

Throughout the 1990s, I figured that if we want to resist this unsettling trend in the government to outlaw cryptography, one measure we can apply is to use cryptography as much as we can now while it’s still legal. When use of strong cryptography becomes popular, it’s harder for the government to criminalize it. Therefore, using PGP is good for preserving democracy. If privacy is outlawed, only outlaws will have privacy.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

Statistics for dummies

This is how we did it for ages

# devtools::install_github("neuropsychology/psycho.R")
library(psycho)

df <- psycho::affective
aov_results <- aov(Adjusting ~ Sex * Salary, data=df)
              Df Sum Sq Mean Sq F value Pr(>F)    
Sex           1   35.9   35.94  18.162 2.25e-05 ***
Salary        2    9.4    4.70   2.376   0.0936 .  
Sex:Salary    2    3.0    1.51   0.761   0.4674    
Residuals   859 1699.9    1.98                     
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
386 observations deleted due to missingness

And this is what R-bloggers recommends

analyze(aov_results)
The effect of Sex is significant (F(1, 859) = 18.16, p < .001) and can be considered as small (Partial Omega-squared = 0.019).
The effect of Salary is not significant (F(2, 859) = 2.38, p = 0.09°) and can be considered as very small (Partial Omega-squared = 0.0032).
The interaction between Sex and Salary is not significant (F(2, 859) = 0.76, p > .1) and can be considered as very small (Partial Omega-squared = 0).

Seriously!

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software, Theology

Das Digitale der Theologie

Christian Henkel, Institut für Ökumenische und Interreligiöse Forschung / Universität Tübingen, hat einen interessanten Beitrag auf feinschwarz verfasst:

Jetzt kommt wieder so ein Digitalisierungsessay. Pünktlich zu Katholikentag, CEBIT oder re:publica rauscht es in der christlichen Blogosphäre und auf Twttr von neuen social media Kampagnen. Schön bunt ist die Welt dort draußen. So bunt, dass ich mich in die monochrome Idylle meiner Kindheit vor dem C64 meines Vaters zurücksehne, 8, 1.

Abgesehen davon, dass der Titel “Digital Denken” nicht so recht passt, ist es ein tiefsinniger Beitrag, der hinter offenem Quellcode den Schöpfer sucht, hinter Blockchain die Autorität, der man Vertrauen schenken kann und hinter Data Mining das Fides quaerens intellectum von Augustinus hinterfragt.

Es lässt sich also eine Debatte um die Digitalisierung führen, die nicht mit Neoanglizismen beginnt und bei der schnellen Internetinfrastruktur auf dem Land endet.

Großartig!

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

Erpressung

Das Reviewsystem der Zeitschrift “Allergy” läuft seit Jahren auf der etwas hausbackenen Manuscript Central Platform. Dann wurde daraus Scholar One, das zuletzt nun Clarivate Analytics einverleibt wurde (dem früheren Geschäftsbereich Intellectual Property und Science von Thomson Reuters).
Bei letzten Einloggen – um ein Manuskript zu reviewen – musste ich dann zwangsweise die DSGVO akzeptieren, ansonsten hätte ich das PDF des Manuskriptes nicht bekommen.

 

 

Clarivate Analytics hat angekündigt diesen Monat auf Amazon Webservices umzustellen. Warum dann überhaupt noch europäische DSVGO abfragten?

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

Export Sente Data

setfile -a b /Users/wjst/Documents/sente.db
cd sente.db/Contents
sqlite3 primaryLibrary.sente601
.output Users/wjst/Documents/sente.sql
sqlite> .dump
sqlite> .schema
sqlite> .quit

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

25. Mai 2018, EU-Datenschutz-Grundverordnung DSGVO: Eine Lösung für das Youtube Problem

Selbst wenn man auf seinem Blog keine Werbebanner, kein Google Analytics und nicht mal Cookies verwendet, bleiben trotzdem einige Aufgaben zu erledigen. Wie ist das mit HTTPS? Ab sofort zwingend. Wie ist das mit Akismet? Erstmal abgeschaltet, da Kommentare nicht erlaubt sind. Und das Kontaktformular? Abgeschaltet. Und Impressum? Ergänzt um zeitlimitierte IP Datenspeicherung.
Dann bleibt also noch die Einbindung externer Seiten zu überarbeiten. Dafür gibt es nun eine Änderung im WordPress Theme Header, welche nur den Content zeigt, denn der Leser aktiv anklickt.

$(document).ready(function(){
  $('iframe[src*="youtube.com"]').each(function(e) {
    var src=$(this).attr('src');
    $(this).attr('name',src );
    $(this).attr('src','/404');
    $(this).after('<img class="me" src="/images/img/externalcontent.png" onclick="$(\'.me\').hide();showyou();"/>');
    $(this).hide();
  });
});
function showyou() {
  $('iframe[name*="youtube.com"]').each(function(e) {
    var src=$(this).attr('name');
    $(this).attr('src',src);
    $(this).show();
  });
}

Was ist der Grund den Iframe nicht nur zu verstecken, sondern auch noch eine Fake URL zu setzen? Auch ein unsichtbarer iframe kann Daten ziehen und Cookies setzen.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Genetics, Software

Is the GWAS reporting of p-values highly flawed?

Since the advent of Nature Genetics I wonder why this journal is publishing articles based on significance and not on effect size. Only recently I found an interesting blog about “the smaller the p-value, the higher the likelihood ratio under the alternative vs the null” fallacy

This statement ignores the fact that under low power conditions, 100% of the significant effects will be based on overestimates of the true effect. This is what Gelman’s Type M error is all about.

Prima vista, I can’t find any error in the argument there. The GWAS power is high  for alleles of 5% frequency but what about 1% or 0.1% minor allele frequency? More about type M errors by Andrew Gelman 2016, basically an error of magnitude – claiming with confidence that theta is small in magnitude when it is in fact large or by claiming with confidence that theta is large in magnitude when it is in fact small. The GWAS publication bias is ultimately leading to systematic Type M errors.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Philosophy, Software

How to drop your Facebook account and create your own timeline with RSS

After leaving Researchgate and Linkedin earlier – never used Instagram and Strava – I am thinking now how to delete also the Facebook account without loosing all my “friends”.

There seems to be a nice solution as I can add any Facebook account to my RSS feed in Miniflux using RSS bridge. This is dead easy, just enter the username and add the resulting feed to the reader.

There is only one downside: All Facebook accounts  (and groups!) need to make their content public available and not just to Facebook and Cambridge Analytica marketing departments.
The fake privacy as well as the assumed exclusivity of Facebook contacts is a built-in design cheat right from the beginning of the social media.

 

CC-BY-NC Science Surf , accessed 29.04.2026
Software

Is the Pareto principle good for science?

The Pareto principle (also known as the 80/20 rule, the law of the vital few, or the principle of factor sparsity) states that, for many events, roughly 80% of the effects come from 20% of the causes.

Is the Pareto principle good for science? Yes, if you are interested in prices, doctorates, honours, achievements, academy membership, AMEX gold card. No, if you are interested in the progress of science, separating wheat from chaff, common goods like educating students. Yes, if you do not have tenure. No, if you have achieved it.

 

CC-BY-NC Science Surf , accessed 29.04.2026