Category Archives: Software

The human disease network (no need to call it diseasome)

There was the 2077 Goh PNAS paper using that title. And it is a sound approach probably better than any division of chapters in Harrison’s Internal Medicine!

A network of disorders and disease genes linked by known disorder–gene associations offers a platform to explore in a single graph-theoretic framework all known phenotype and disease gene associations, indicating the common genetic origin of many diseases. Genes associated with similar disorders show both higher likelihood of physical interactions between their products and higher expression profiling similarity for their transcripts, supporting the existence of distinct disease-specific functional modules. We find that essential human genes are likely to encode hub proteins and are expressed widely in most tissues.

I found this on a slide at the recent vitamin D congress in London and was just interested to see, how often this paper has been cited. So far as I remember only the Barabasi update. And the result is impressing Continue reading The human disease network (no need to call it diseasome)


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Avoid spinners

I see spinners everywhere – although I once learned that this is just poor website design. There are even spinner factories to create you own custom waiting room.
gif
As I am doing a lot of time consuming jpg manipulation here and didn’t want to further increase any server overhead, I went back to rather old fashioned method – the turning slash known from old UNIX and DOS times. It expands my previous article on avoid-browser-flickering-with-dark-backgrounds writing to the preloader div and stopping after loading the iframe.

var str = "|/-\\";
var i = 1;
function myLoop () {
   setTimeout(function () {
      j=str.charAt(i%(str.length));
      $('#preload').text( i ) ;
      i++;
      if (i<99) myLoop();
   }, 150)
}
myLoop(); 
$(function(){
    $('#iframe').load(function(){
        i=99;
    });
});

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“Keep left on bike path” – an old Garmin 60 CSX and a brandnew Openfietsmap

This is the combination that I tried today on a cycle route across Munich. And it is funny to see that there are some hidden bike paths that I was not aware off – the picture shows Schloß Blutenburg where I did not know this track along Pippinger Straße.

DSCF2516

Sure, many cycle paths are not usable Continue reading “Keep left on bike path” – an old Garmin 60 CSX and a brandnew Openfietsmap


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Seite an Seite einschlafen

Aus Seeberger, Schamlose Neugier, Integral München, 2012, S.213:

Es gibt Menschen deren Weltbild gleicht einem Anwesen, bei dem man “eine Mauer um sich herum baut, diese mit Stacheldraht und Glassplittern versieht und Patrouillen ausschickt, um eingebildete oder echte Bedrohungen zu verjagen” wie der Schriftsteller Göran Tunström einmal schrieb. Während bei anderen die Weltanschauung wie “ein großer Hof ohne Mauer und Zaun ist, wo die tagsüber frei umherstreunden Ansichten abends ruhig nach Hause trotten, um Seite an Seite einzuschlafen”.


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Avoid browser flickering with dark backgrounds

There is no ultimate solution to avoid the white phase when switching pages in the browser.

Here is a rather simple strategy using embedded pictures. This is usually not recommended as the necessary base64 encoding includes quite some overhead. It influences, however, the browser rendering by basically blocking the download of the remaining page which is probably the anti-flickering effect.

echo '<img src="data:image/png;base64,';
echo base64_encode(file_get_contents($file));
echo '"/>';

Works mostly, but not always. Another interesting approach has been suggested by another user, eg decreasing page loading time by async loading before switching between pages. I didn’t like that so much as it keeps the pages in your browser piling up.

So finally I did a small page only with a large iframe that is covered by a black div and removed only after loading the iframe content. Works on all tested browsers.

<style>
#preload {
background:black;
width:100%;
height:100%;
z-index:2;
top:0px;
left:0px;
position:absolute;
}
</style>

<script>
$(function(){
   $('#iframe').load(function(){
    $(this).show();
    $('#preload').fadeOut();
  });
});
</script>

<div id="preload">loading...</div>

<iframe src="http://external.url.de" id="iframe">
</iframe>

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Let your visitors switch background color

There seem to be million of ways to do that – here is the most parsimonious solution that works for me even under difficult conditions and in different browsers.

// should be run in a $(document).ready(function(){ bracket });
// if there is no cookie we set one
if (document.cookie.indexOf("color")!== -1 {
  document.cookie = "color=white";
}
// we need a body class without any background definition
// and a class for body.black that has background:black
if (document.cookie.indexOf("black") === -1) {
  // switch to the new .black class
  $("body").toggleClass("black");
  // this is also possible in the iframe
  $(#iframe").contents().find("body").toggleClass("black");
}
// link or whatever is being clicked for the effect
$(".place").click(function () {
if (document.cookie.indexOf("white") !== -1) {
  document.cookie = "color=black";
}
else {
  document.cookie = "color=white";
}
// reload page with a small delay
setTimeout( function() { location.reload() }, 250 );

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Why I believe in twin studies

20120609-DS7_0692

Zwillingstreffen im Pillerseetal  7. Juni 2012 - 9. Juni 2012

These are some pictures that I took roughly two years ago on twin meeting in Austria. Twin studies give us some unique opportunities like in this recent paper

We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes.


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WordPress: Multiline site title instead of tagline

I found it hard to change the layout of the tagline in my WordPress Twentyfourteen child theme as the element sits in a different hierarchy. But fortunately we can add text also from the CSS stylesheet (which is not visible in the sourceode!) using the content tag. It does not accept standard HTML while the special formatting is shown on stackoverflow.

.site-title :after {
	font-size: 25px;
    content: "\00000aBut let your communication be Yea, yea;\00000aNay, nay: for whatsoever is more than these cometh of evil";
    white-space: pre;
}

The reason for that? Just a quick fix.


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Veracity

It is a rather old topic here at Science Surf –searching for truth in science while here is a fresh new look.  How can we trust twitter messages and alike, is there any truth in big data?  What is just an internet meme?  Or a phenomenon — a meaning what is experienced as given? A pheme? A new EU project explains Continue reading Veracity


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Wissenschaftsbetrug und soziale Akzeptanz

Mag sein, daß es immer mehr Wissenschaftsbetrug gibt. Es kann aber auch sein, daß nur das Bewusstsein geschärft ist. Es würde mich jedenfalls nicht wundern, daß der erhöhte Leistungsdruck statt zu weiteren Höchstleistungen zu noch mehr Betrug führt.
Aus einem ganz anderen Gebiet kommt nun eine Erklärung, warum es mit der Moral bei uns doch nicht so weit her ist.

Steuerhinterziehung gilt vielen in Deutschland als Kavaliersdelikt … “Die Steuerpflicht ist keine Norm, die man verinnerlicht hätte. Man trifft erst im Erwachsenenalter auf sie”, sagt Carsten Ullrich … Erstens lässt sich eine Norm wie diese relativ angstfrei missachten … Zweitens ist eine solche Norm, die sich nur intellektuell nachvollziehen lässt, “schwer zu verstehen” … In den neunziger Jahren ordnete ein soziologisches Standardwerk noch 18 Prozent der Bevölkerung dem Milieu der “Konventionalisten” zu, denen Pflicht und Akzeptanz am wichtigsten sind.

Die wissenschaftlichen Normen des exakten Messens und des vourteilsfreien Berichtes kann man nicht angstfrei missachten. Bei aufgeflogenem Betrug ist das Karriereende sicher.
Aber es stimmt natürlich, daß wissenschaftliche Redlichkeit eine relativ spät erfahrbare Norm ist, die sich nur intellektuell nachvollziehen lässt.
Der DHV will Wissenschaftsbetrug strafbar machen während Milos Vec in der FAZ davon nicht recht überzeugt ist und auf die Probleme einer strafrechtlichen Verfolgung hinweist.


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We cannot dispense with palliative measures (Freud)

Life, as we find it, is too hard for us; it brings us too many pains, disappointments and impossible tasks. In order to bear it we cannot dispense with palliative measures. ‘We cannot do without auxiliary constructions’, as Theodor Fontane tells us in his novel Effi Briest.

Sigmund Freud Religion as a mass delusion. Civilization and its Discontents (1931). The  photo was taken in Vienna 1985, Burggasse not Berggasse…

Continue reading We cannot dispense with palliative measures (Freud)


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Forcing two divs in one row

In my picture gallery I show two divs side by side. Div1 is variable and needed only on a few pages. Div2 is large, complicated and takes quite some time to load as there are numerous pictures and jquery actions.
div
Rather simple setup, isn’t it? The rendering should be smooth (both divs loading at final position and not jumping around at the end of page loading) and fluid (working on smaller devices as well) and without any dynamic stylesheet language.
This simple task turned out to be complicated. Continue reading Forcing two divs in one row


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Der Ramstetter Faktor 10,0613083

Jahrelang mussten sich das die ADAC Motorwelt Leser antun, jeden Monat neu, 15 Jahre lang, den einseitigen Autolobbyismus des Michael Ramstetter. Und jetzt ist sie auch quasi amtlich

die Zahl, mit der der mittlerweile ausgeschiedene ADAC-Pressechef Ramstetter die tatsächlich abgegebenen Stimmen bei der ADAC-Wahl zum “Gelben Engel” aufgepimpt hat

Der Spiegel hat wohl etwas gerundet in seinem Artikel, Continue reading Der Ramstetter Faktor 10,0613083


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