Michael Clerx
@michaelclerx.com
I do sums to learn why heart cells beat. Computational biologist. Biological computer. Sometimes does experiments. Whippet owner. Makes bad jokes. He/him.
I, um...
I went on a website - not a dodgy one - right? And
Well
And it showed me an ad
I went on a website - not a dodgy one - right? And
Well
And it showed me an ad
October 14, 2025 at 10:45 PM
I, um...
I went on a website - not a dodgy one - right? And
Well
And it showed me an ad
I went on a website - not a dodgy one - right? And
Well
And it showed me an ad
A more optimistic way of plotting the same data, shows that we've gone from ~95% no-code in 2000, to 30.2% of models published with procedural code in 2025, and 14.5% published with (even better!) declarative code.
October 13, 2025 at 10:08 PM
A more optimistic way of plotting the same data, shows that we've gone from ~95% no-code in 2000, to 30.2% of models published with procedural code in 2025, and 14.5% published with (even better!) declarative code.
To make it pretty, I had to group a lot of formats under "Other". To get a better view of what "other" formats are, I made this graph excluding the big three (no code, matlab, cellml). From top to bottom it goes Myokit (yay!), C++, simBio, C, CARP, Delphi, Fortran, Visual basic, and Neuron
October 13, 2025 at 10:08 PM
To make it pretty, I had to group a lot of formats under "Other". To get a better view of what "other" formats are, I made this graph excluding the big three (no code, matlab, cellml). From top to bottom it goes Myokit (yay!), C++, simBio, C, CARP, Delphi, Fortran, Visual basic, and Neuron
So with the parsing (and a standardised format in the markdown) in place, you can start doing some fun graphs!
Fun - but heavily caveated. This is based on what is on my list, not what exists out there. But I had a go at least 🤷. The entries outside of "No code" are hopefully a good lower bound
Fun - but heavily caveated. This is based on what is on my list, not what exists out there. But I had a go at least 🤷. The entries outside of "No code" are hopefully a good lower bound
October 13, 2025 at 10:08 PM
So with the parsing (and a standardised format in the markdown) in place, you can start doing some fun graphs!
Fun - but heavily caveated. This is based on what is on my list, not what exists out there. But I had a go at least 🤷. The entries outside of "No code" are hopefully a good lower bound
Fun - but heavily caveated. This is based on what is on my list, not what exists out there. But I had a go at least 🤷. The entries outside of "No code" are hopefully a good lower bound
POV: You realise building a comfy seat opposite the fridge was a bad idea
July 27, 2025 at 8:20 PM
POV: You realise building a comfy seat opposite the fridge was a bad idea
So big, that if you mix and match experiments, you can find midpoints of inactivation exceeding those of activation - clearly not physiological. Luckily, 150 experiments provided both values, so that we could plot one against the other.
We found a striking correlation, with a slope close to 1.
We found a striking correlation, with a slope close to 1.
July 16, 2025 at 4:55 PM
So big, that if you mix and match experiments, you can find midpoints of inactivation exceeding those of activation - clearly not physiological. Luckily, 150 experiments provided both values, so that we could plot one against the other.
We found a striking correlation, with a slope close to 1.
We found a striking correlation, with a slope close to 1.
We took 117 studies that contained measurements of the mean midpoints of activation (157 values) and inactivation (165 values) in expression systems. Though the papers were all about mutants, we looked only at the control (wild-type) values.
The variation in these was way bigger than we expected.
The variation in these was way bigger than we expected.
July 16, 2025 at 4:55 PM
We took 117 studies that contained measurements of the mean midpoints of activation (157 values) and inactivation (165 values) in expression systems. Though the papers were all about mutants, we looked only at the control (wild-type) values.
The variation in these was way bigger than we expected.
The variation in these was way bigger than we expected.
INa is a major determinant of cardiac excitability and propagation, and small changes to its electrophysiology are associated with increased arrhythmic risk. It is commonly studied by expressing the channel gene SCN5A in HEK or sometimes CHO cells, using an analysis like in panels B and C below.
July 16, 2025 at 4:55 PM
INa is a major determinant of cardiac excitability and propagation, and small changes to its electrophysiology are associated with increased arrhythmic risk. It is commonly studied by expressing the channel gene SCN5A in HEK or sometimes CHO cells, using an analysis like in panels B and C below.
I wonder what percentage of the internet is now dedicated to explaining the internet
July 13, 2025 at 1:30 AM
I wonder what percentage of the internet is now dedicated to explaining the internet
Angrily points at drawing: this represents an opportunity! Don't you know an opportunity when you see it?
June 27, 2025 at 10:34 AM
Angrily points at drawing: this represents an opportunity! Don't you know an opportunity when you see it?
Looking through some old slides
June 25, 2025 at 3:53 PM
Looking through some old slides
I understand every step of the naming process, and yes yup sure okay, but.
The end result.
The university school of education! That's where I took my lessons, me!
The end result.
The university school of education! That's where I took my lessons, me!
June 25, 2025 at 2:13 AM
I understand every step of the naming process, and yes yup sure okay, but.
The end result.
The university school of education! That's where I took my lessons, me!
The end result.
The university school of education! That's where I took my lessons, me!
Have some whippets instead
June 25, 2025 at 1:11 AM
Have some whippets instead
Imagine this will be going up a bit
June 22, 2025 at 2:25 PM
Imagine this will be going up a bit
Her mum's just walked through the door.
January 26, 2025 at 1:15 AM
Her mum's just walked through the door.
Last weekend in the lake district.
Not my photo (though one is my dog) but will pass on any likes 😄
Not my photo (though one is my dog) but will pass on any likes 😄
January 23, 2025 at 9:34 PM
Last weekend in the lake district.
Not my photo (though one is my dog) but will pass on any likes 😄
Not my photo (though one is my dog) but will pass on any likes 😄
