Tag Archives: software

Parallelized computer code and DNA transcription

At stackexchange there is a super interesting discussion on parallelized computer code and DNA transcription (which is different to the DNA-based molecular programming literature…)

IF : Transcriptional activator; when present a gene will be transcribed. In general there is no termination of events unless the signal is gone; the program ends only with the death of the cell. So the IF statement is always a part of a loop.

WHILE : Transcriptional repressor; gene will be transcribed until repressor is not present.

FUNCTION: There are no equivalents of function calls. All events happen is the same space and there is always a likelihood of interference. One can argue that organelles can act as a compartment that may have a function like properties but they are highly complex and are not just some kind of input-output devices.

GOTO is always dependent on a condition. This can happen in case of certain network connections such as feedforward loops and branched pathways. For example if there is a signalling pathway like this: A → B → C and there is another connection D → C then if somehow D is activated it will directly affect C, making A and B dispensable.

Of course these are completely different concepts. I fully agree with the further stackexchange discussion that

it is the underlying logic that is important and not the statement construct itself and these examples should not be taken as absolute analogies. It is also to be noted that DNA is just a set of instructions and not really a fully functional entity … However, even being just a code it is comparable to a HLL [high level language] code that has to be compiled to execute its functions. See this post too.

Please forget everything you read from Francis Collins about this.

How to regulate ChatGPT use

With the even increasing use of ChatGPT there is also a debate not only on responsibility but also crediting findings to individual authors.

The artificial-intelligence (AI) chatbot ChatGPT that has taken the world by storm has made its formal debut in the scientific literature — racking up at least four authorship credits on published papers and preprints.  Journal editors, researchers and publishers are now debating the place of such AI tools in the published literature, and whether it’s appropriate to cite the bot as an author.

Software recognition of AI generated text is not 100% accurate in particular if there are less than 1000 characters available. And of course, scientific texts will be always edited to evade the classifier.

Having discussed here this issue yesterday, we think that we need some kind of software regulation – sending the generated AI output not only to the individual user but keeping a  full logfile of the output that can be accessed, indexed and searched by everybody.

 

 

 

Data and methods available? Forget it!

Bergeat 2022

Data were available for 2 of 65 RCTs (3.1%) published before the ICMJE policy and for 2 of 65 RCTs (3.1%) published after the policy was issued (odds ratio, 1.00; 95% CI, 0.07-14.19; P > .99).

Danchev 2021

Among the 89 articles declaring that IPD would be stored in repositories, only 17 (19.1%) deposited data, mostly because of embargo and regulatory approval.

Gabelica 2022 (visualization @ Nature)

Of 3556 analyzed articles, 3416 contained DAS. The most frequent DAS category (42%) indicated that the datasets are available on reasonable request. Among 1792 manuscripts in which DAS indicated that authors are willing to share their data, 1670 (93%) authors either did not respond or declined to share their data with us. Among 254 (14%) of 1792 authors who responded to our query for data sharing, only 122 (6.8%) provided the requested data.

The same issue applies also to software sharing  where less than 5% of all papers is depositing code. And whenever they deposit software, it is even not running anymore a few years later as operating systems and libraries changed.

Both issues took me many years of my scientific life. It is recognized by politics in Germany but also the most recent action plan looks  … ridiculous. Why not making data and software sharing mandatory at time of publication?

Sometimes it is better to switch bikes not gears

My 3 favorite programs? R, Bookends and Exposure.

The first choice is Rstudio (since 2012, being a long time SAS user). Here is the most recent JJ Allaire keynote

 

I was a bit with late with Bookends in 2018 (being a long time Sente user) but here is an introduction by Jon Ashwell.

 

And I am currently migrating to Exposure (after having used Lightroom for 13 years) by Jeff Butterworth

 

Life changes every day while it is sometimes better to switch bikes not gears.

Leaflet.js – layer order, layer address and links

Leaflet is great for mapping in epidemiology with quick results of just cut & pasting a few lines. Problems do start, however, whenever running a more advanced project. It’s a pain, as plugins overwrite functions and basic css layouts. Or layers do not allow clickable links (as propation is being prohibited). Or geojson data that are rejected for whatever reason.
A showcase project, that had been planned for 2 days, took more than 1 week as the documentation is frequently unclear, incomplete and often hard to understand without any (jsfiddle) example. Numerous Google searches helped, as well as peaking into the sourcecode, while also other stack overflow posters have been very helpful. Continue reading Leaflet.js – layer order, layer address and links

Better figures

A recent paper identifies 10 rules for better pictures. As I have also given several lectures on that topic, I was excited what the authors think…
1. Know your audience. This is trivial as you never know your audience.
2. Identify your message. True and not true at the same time. True as it makes your findings more evident – not true if you are allowing a reader to find his own message.
3. Adapt the figure to the support medium. Trivial. May be very time consuming.
4. Captions are not optional. Absolutely true, I also suppport good captions – mini stories for those who can’t read the whole text.
5. Do not trust the defaults. Trivial. No one does.
6. Use color efficiently.  Not really,  avoid colors for those of us who are colorblind and to avoid expensive page charges.
7. Do not mislead the reader. Why should I?
8.  Avoid Chartjunk. Absolutely. Most frequent problem.
9. Message trumps beauty. Sure, form follows function.
10. Get the right tool. Maybe correct while the further recommendations look like a poor man’s effort to make his first graphic at zero cost: Gimp, Imagemagick, R…

Mapfactor Navigator: Convert you POIs

I am currently switching to Mapfactor Navigator mainly to use now also offline Open Street Maps.
The main problem is to get all those old waypoints converted. Unfortunately it is confusing what developers but users are reporting on different forums. MN obviously used different tools at different times and even different directories.

Before you start, get the most recent version Continue reading Mapfactor Navigator: Convert you POIs

PLINK: Bug or feature?

I am struggling now for 4 weeks with some unusual behaviour in PLINK that gives me different results with a trait of the alternate phenotype files either by calling that trait directly

plink –file mydata –tdt –pheno pheno2.txt –mpheno 1

or from a loop over all traits

plink –file mydata –tdt –pheno pheno2.txt –all-pheno

It seems that I am working with different numbers at both occasions – click to enlarge the log Continue reading PLINK: Bug or feature?

Playing with your browser

Some blog authors are nuts about protecting their web site from copying files. There are many ways to protect your site – but only one really good (publish nothing). I often see small javascripts that disable the ability to right-click where javascript.about.com has a much simpler solution:

<body oncontextmenu=”return false;”>

Please try a right click now…
If you are fooled by a web author in such a way, what could you do? tech-recipes has the answer: Of course, we can use javascript to turn it back on.

When visiting the offending website, type the following into the URL bar of your browser:
javascript:void(document.oncontextmenu=null)

Happy browsing, yea, yea.