Category Archives: Software

Allergy, Software

Journal of Allergy

Being spammed by a company called Hindawi for many years, I tried to find out a bit more about one of their journals called “Journal of Allergy”. The website http://www.hindawi.com/journals/ja says

Journal of Allergy is a peer-reviewed, open access journal that publishes original research articles, review articles, and clinical studies in all areas of allergy. Journal of Allergy currently has an acceptance rate of 43%. The average time between submission and final decision is 59 days and the average time between acceptance and final publication is 34 days.

According to their own description, they are located in Cairo and employ some 200 to 1,000 employees. Hindawi seems to be the name of one of their founders. In some other web sources they claim  410 Park Avenue, 15th Floor, New York, USA, as their address.  Google Streetview shows at  that address a 11+2 floor building with Chase Manhattan Bank located at the ground floor.
Only 40 or so of the 500+ Hindawi journals have any impact factor associated with.
Declan Butler at Nature already wrote about these kind of journals:

Open-access publishers often collect fees from authors to pay for peer review, editing and website maintenance. Beall asserts that the goal of predatory open-access publishers is to exploit this model by charging the fee without providing all the expected publishing services. These publishers, Beall says, typically display “an intention to deceive authors and readers, and a lack of transparency in their operations and processes”.

At the moment, the Journal of Allergy is not being black listed by Beall (while Hindawi had been in the past). “Journal of Allergy” should not be confused with “The Journal of Allergy”[Jour] that has 1514 PUBMED entries while the “Journal of Allergy”[Jour] has only 157 entries so far. Is this an “intention to deceive authors and readers”?
The most recent issue appears as of “Epub 2014 Apr 6”, the first one as “Epub 2009 Jul 2”, so the company basically publishing 2-3 papers per month.
The Pubmed Analyzer are not very informative here. The whole “Journal of Allergy” has accumulated only 135 citations in the past 5 years (not an impressive figure as I have authored more than a dozen single papers that have received all more citations than the whole journal).
The extreme low citation rate and the missing impact factor may not be taken as an indicator that all papers are of poor quality but raises serious doubts.
The next question therefore is: Does the journal run a state of the art review process? The website list the following 24 scientists on the review board:

William E. Berger, University of California, Irvine, USA
Kurt Blaser, Universität Zürich, Switzerland
Eugene R. Bleecker, Wake Forest University, USA
Jan de Monchy, University of Groningen, The Netherlands
Frank JP Hoebers, MAASTRO Clinic, The Netherlands
Stephen T. Holgate, University of Southampton, United Kingdom
S. L. Johnston, Imperial College London, United Kingdom
Young J. Juhn, Mayo Clinic, USA
Alan P. Knutsen, Saint Louis University, USA
Marek L. Kowalski, Medical University of Lodz, Poland
Ting Fan Leung, The Chinese University of Hong Kong, Hong Kong
Clare M Lloyd, Imperial College London, United Kingdom
Redwan Moqbel, University of Manitoba, Canada
Desiderio Passali, University of Siena, Italy
Stephen P. Peters, Wake Forest University, USA
David G. Proud, University of Calgary, Canada
Fabienne Rancé, CHU Rangueil, France
Anuradha Ray, University of Pittsburgh, USA
Harald Renz, Philipps University of Marburg, Germany
Nima Rezaei, Tehran University of Medical Sciences, Iran
Robert P. Schleimer, Northwestern University, USA
Massimo Triggiani, Università degli Studi di Napoli Federico II, Italy
Hugo Van Bever, National University of Singapore, Singapore
Garry M. Walsh, University of Aberdeen, United Kingdom

Unfortunately this list is not identical to the editor names that are being listed directly on the PDFs ( eg the academic editor RM is not being listed at the web front). The  above editor list includes indeed some well respected scientists but there are also others that show their Hindawi affiliation as their first hit on Google only. As I know 7 of the 24 persons, I decided to email them a short 6 item questionnaire via Surveymonkey.

When did you start your role as an editor?
2009, 2010, 2011, 2012, 2013, 2014
2. What is your role there?
Leading editor- supervising associate editors
Editor – assigning papers to reviewes, holding final decision Reviewer – reading and scoring papers
Sonstiges (bitte angeben)
3. How many papers have you been dealing with?
0, 1, 2, 3, 4, 5 or more
4. How many papers did you accept?
nearly none, about half, most, all
5. Are you being paid for that work?
no, yes, don’t want to tell
6. Is this a serious journal?
no, yes, don’t know

2 of my 24 emails bounced- some of the members of the editorial board are already retired.
19 did not respond. I believe they will show the same behaviour when being addressed by Hindawi.
1 editor sent me a personal email saying that he will resign from the board. It will be interesting to see when the list of editors will be changed, I already started a change detection.
3 editors answered the mini survey: Editor #1 started in 2010, has been dealing with more than 5 papers, accepted most, is not paid and believes it is a serious journal. Editor #2  started in 2009 with all other responses being identical.  Editor #3 started also in 2009 but accepts only half of the papers.
It doesn’t come unexpected that these 3 motivated editors believe in a regular review process. I fear, however, that most editors either do not work for the journal (anymore) or are not motivated to spend even 3 minutes for the quality control of their work.
Without any transparent review process like that at the BMC journals, we can not judge from the outside if there is any review process. The names of the individual reviewers are unknown, and even contacting the authors would not help as they don’t have an interest to reveal that they get a paper published without any review process.

As a library one could order printed copy ( e.g. 20 articles per year for $395 ) although I could not locate any library in the world that has any subscription to this journal.
As an author I would be charged $800 per PDF. There seems to be no major text editing included in the publication process, what you get for your $800 is a quickly reformatted text, a PUBMED entry and a PDF sitting at a cloud server for an unknown storage time. My estimate for that service is $10.

Declan Butler developed a check list of serious publishers and journals. So we can now use that check list to judge this journal.

Check that the publisher provides full, verifiable contact information, including address, on the journal site. Be cautious of those that provide only web contact forms.

FAILED (PARTIALLY)

Check that a journal’s editorial board lists recognized experts with full affiliations. Contact some of them and ask about their experience with the journal or publisher.

FAILED (PARTIALLY)

Check that the journal prominently displays its policy for author fees.

PASSED

Be wary of e-mail invitations to submit to journals or to become editorial board members.

FAILED (SPAMMER)

Read some of the journal’s published articles and assess their quality. Contact past authors to ask about their experience.

FAILED (POOR QUALITY)

Check that a journal’s peer-review process is clearly described and try to confirm that a claimed impact factor is correct.

FAILED (NO IMPACT)

Find out whether the journal is a member of an industry association that vets its members, such as the Directory of Open Access Journals (www.doaj.org) or the Open Access Scholarly Publishers Association (www.oaspa.org).

PASSED

Another set of guidelines for fake journals is available at Wikipedia. Complaints that are associated with predatory open-access publishing include

Accepting articles quickly with little or no peer review or quality control, including hoax and nonsensical papers.

CAN NOT BE DECIDED YET

Notifying academics of article fees only after papers are accepted.

FALSE

Aggressively campaigning for academics to submit articles or serve on editorial boards.

TRUE

Listing academics as members of editorial boards without their permission, and not allowing academics to resign from editorial boards.

UNCLEAR

Appointing fake academics to editorial boards.

FALSE

Mimicking the name or web site style of more established journals.

TRUE

Verdict: The journal does not pass the Butler criteria of a scientific journal.

Comment: I do not see any major problem if an open access journal is publishing all manuscripts it receives, leaving the final decision of being good or bad science to a post-publication review process. I see, however, a major problem if any pre-publication review process is being assumed for Pubmed listed papers (and paid for) while being never documented in a transparent way.

Addendum: Change log editor page

 

CC-BY-NC Science Surf , accessed 09.05.2026
Joke, Software

How our personal data are being traded

Tom Brewster had an interesting idea: selling hsi own data. Why should anyone else make money with it?

When I decided to sell the secret details of my personal life, I had high hopes I’d get a willing buyer. It didn’t go well.
I had been curious to see if I could make money from my online information – something that data brokers across the world are doing every day; collecting it, combining it with others’ information and flogging it to marketing firms or anyone willing to pay. So I put myself on eBay.

The article is really interesting to read, yea, yea.

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

ChipMe

I am excited to be part of a new COST action So far only the EU description has been online while now also the brandnew website can be reached at chipme2.promoscience.com (twitter channel is @IS1303CHIPME).

Bildschirmfoto 2014-05-08 um 14.13.30

From the official project description

The falling cost of genome sequencing is making genetic information more easily accessible to the ordinary citizen. The proliferation of different actors in COST countries and beyond, engaging with the generation and interpretation of genetic data represents a tremendous opportunity but also a new challenge for society. The public health care system will increasingly be asked to provide interpretation and counselling relating to genetic information that has been generated privately and to satisfy the legitimate curiosity of participants in large-scale population genetic research. Existing ethical and regulatory frameworks may not be suitable to allow an efficient and ethical meeting of demand and supply of genetic knowledge and health, as well as a virtuous interaction between public and private actors. This Action aims to improve the state of the art by creating a community of researchers and stakeholders and linking existing initiatives which bring critical expertise in bioethics, social studies of science and technology, genetic technology, information and communication technology, stakeholder deliberation, and patient centred initiatives (PCI).

 

CC-BY-NC Science Surf , accessed 09.05.2026
Philosophy, 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) →

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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;
    });
});

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

“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 →

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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”.

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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>

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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 );

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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.

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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.

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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.

 

CC-BY-NC Science Surf , accessed 09.05.2026
Software

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) →

 

CC-BY-NC Science Surf , accessed 09.05.2026