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The paper by Lobo and Levin is an attempt to learn a model that represents the inner workings of a biological system by fitting parameters to data. This is a common topic in "systems biology", a model-based approach to studying biology that is popular in some fields. Even for small systems, this is a phenomenally hard problem. Unlike most machine learning ...

20

The fruit, sadly, does not hang so low. Short version Lobo et al (the work you refer to) is a nice and not especially novel application of basic Systems Biology modeling approaches to the wound healing system in flat worms. The main barrier to the wider application of such work is the lack of the necessary experimental data. Lobo et al themselves don't ...

13

Overview Modelling has come on leaps and bounds over the last decade or so and in many cases has acted as a sometimes viable, and inexpensive substitute for experimental structures. How do you know when you get it right? Ultimately, one still needs experimental evidence to know when a model generated in silico is right. But there are ways of scoring a ...

9

There is one book that will perfectly suits your needs: A biologist's guide to Mathematical Modeling in Ecology and Evolution, by Sally Otto It is a very good book that is very easy to understand and in the meantime goes pretty far (It ends with the use of diffusion equation in Evolutionary Biology). I highly recommend it. It covers: How to create a ...

9

Mechanistic model answers the how question. These models are usually biophysically detailed, and designed to be causal. Say you discovered a linear relation between blood pressure drug and heart rate. This would be a statistical model. It doesn't tell you how the two are related biophysically. One could build a detailed model that describes intermediate ...

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The two most common families of scoring matrices are BLOSUM and PAM. Each of them has a score for every possible alignment combination between the 20 standard amino acids1. They both do more or less the same job but have been derived using different approaches. BLOSUM matrices (image taken from Wikipedia) The BLOSUM matrices are built from actual alignments ...

8

I don't believe you'll ever find the first work in bioinformatics (or computational biology, as you put it), however the field really began in the times of accumulating data about protein biochemistry. Computational biologists (before they had access to the computer) would be writing and analyzing morphologies and types of proteins with pencil and paper. ...

8

Another nomination, if you include infectious disease epidemiology as part of biology and hence computational simulations of epidemics as part of computational biology: Measles periodicity and Community Size, M. S. Bartlett, J. Roy. Stat Soc. A, 120(1), 1957. The computations were run on the Manchester computer. Possibly the most entertaining part of the ...

5

The question appears interesting and made me think but I might not fully understand it. Let me know if I am answering your question. Genetic algorithm vs simulation of evolutionary processes I think that the whole issue comes from a confusion between the concept of simulating evolutionary processes and the use of genetic algorithm (type of optimization ...

5

Although work in those areas is definitely all related, there are some kind of general differences in how those labels tend to be used, and I'll take a stab at defining them: Mathematical ecology - this is typically the creation of theoretical models composed purely from math (i.e. not stochastic computer models). Examples include a lot of classics from ...

5

Though I have not found direct access to a model (which is what I'm really looking for), I have found evidence of such modeling efforts. The CDC apparently put out a risk-assessment report in mid July discussing the results of such epidemiological modeling (reported by FivethirtyEight, ABC and others). The report (available here), suggests that the risk of ...

5

Such a model would require a fairly detailed and complete biological inventory as well as detailed knowledge of the species' interactions, and a detailed map of the physical and chemical makeup of the location or region... I suggest reading about the The Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES).1 This ...

4

If you abstract enough, anything cam be considered as a computational device. The issue with doing this with cells is the sheer number of variables. For any given cell, the following internal variables exist: Internal ion concentrations for dozens of ions of importance importance Internal concentrations of hundreds or thousands of various simple organic ...

4

SBML follows in the same vein as XML, in that it provides a standardized and flexible method for structuring information. XML and its ilk aren't just for making web pages, they're for sending structured datasets between systems and programs (in fact, XML is a fairly common configuration format). Why? Because the structure makes parsing simple (well, simple-...

4

This is a tough topic, have a look at the following references and see, if they can help you: Structural modelling and dynamics of proteins for insights into drug interactions. Ligand entry pathways in the ligand binding domain of PPARγ receptor Pathway and mechanism of drug binding to G-protein-coupled receptors Molecular Dynamic Simulation and Inhibitor ...

4

There have been several Turing machines constructed using DNA computing. One of these machines has been used to solve the boolean satisfiability problem, another was used to solve the bounded post correspondence problem, both NP-hard combinatorial problems which are difficult for conventional computers to solve. Also, a DNA computer was constructed that ...

4

A scoring matrix is used to compute a score for finding identical 3-letter words or similar 3-letter words that takes into account the liklihood of one being related to another. Although these matrices are empirical, they encompass factors like the number of mutations required (which is why there are different matrices for different extents of divergence) ...

4

Biology is a large field of knowledge! As you give examples drawn from population biology (logistic population growth and Lotka-Voltera models), I will assume you are mainly interested in ecology and evolution. For analytical models used in ecology and evolution, I highly recommend the book A Biologist's Guide to Mathematical Modeling in Ecology and ...

4

Let's take the example of the model bacterium E. coli, for which one can find the numbers for a wet cell of a dry mass of 0.28pg. If you have a feeling for how much smaller the smallest known bacterium is compared to E. coli, you can ballpark things. The number of carbon atoms in a single E. coli cell is approx. 7x10^9 carbon atoms. The ratio of elements ...

4

For the logistic equation, $$\frac{\mathrm{d}N(t)}{\mathrm{d}t} = rN(t)\left(\frac{K - N(t)}{K}\right)$$ the solution that allows you to calculate population population size at any time is: $$N(t) = \frac{N(0)Ke^{rt}}{K - N(0) + N(0)e^{rt}}.$$ Looking at this equation algebraically with a set of knowns—$K$, $t$, and $N(t)$—and a set of unknowns—$r$ and $N(0)$...

3

Christian, great idea to ask this question here before taking important decisions. Are those media articles a hype? Yes. Over the last 10 years I constantly see those hype stories in media about "revolutionary" large-scale-study/big data projects with mind-blowing numbers (gigabases, teraflops, terabytes, thousands of papers and hundreds of genes). ...

3

The equation in the OP has been updated to $(y-a)^2(y-a\theta)$ which yields the correct expansion. Therefore, by equating the coefficients, we obtain \begin{align} \alpha &= (2+\theta)a\tag{1}\\ \rho/\beta^2 &= a^2(1+2\theta)\tag{2}\\ \alpha/\beta^2 &= a^3\theta\tag{3} \end{align} Using equations (1) to (3), we get the desired $\rho$ and \$\alpha\...

3

A Markov model is a description of a system that follows a Markov process. In a Markov process the next state of the system is a function of its current state and does not depend on where from and how it started. For example Brownian motion can be called a Markov process. The transition from current state to next state is described by probabilities. So to ...

3

Absolutely, the two I've had the most success are working with a radiolabeled and a fluorescently labeled version of the drug. Many drugs autofluoresce as well and this can be easily tracked. When it's labeled as mentioned above microscopy or a luminometer, spectrophomoter or a scintillation counter can evaluate fractions or whole cells, or purified ...

3

Here are a few metrics you can calculate to get you started. You can use R to perform these calculations. Net Diversification Rate (r) Net diversification rate is (rate of speciation - rate of extinction). You can calculate it using the bd.ms or bd.km functions in the geiger package for R. r = 1: r = 2: Tree Imbalance: Colless index (I) Colless's ...

3

First I'll answer this question on the assumption that you are learning or about to learn python (perhaps because you have heard it's become popular in bioinformatics) and you wish to know whether it can be applied to this problem. The answer is: almost certainly, yes. Python is a programming language of the type that can be used to automate the solution of ...

3

I agree with the previous answer. You can certainly write a solution in python, but have to formulate it as an algorithm first. Doing so will enable us to suggest an actual solution. Also, I wanted to suggest that posting this questions on a forum with bioinformatics focus (biostars.org) may yield better feedback.

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My boss is a big fan of Repast HPC, but since Repast is a C++ framework it might not be the right choice for you. It takes a loooong time to write a good C++ program (even for someone who already knows the language fairly well), although it will run very quickly once it's written. A one or even two year long Master's program will end up going by surprisingly ...

3

Depending on your definition of computational biology (e.g. bioinformatics and mathematical modelling can be quite different), there is an oft-cited reference to Alan Turing's work after the second world war, modelling what he called "morphogens" in the emergence of mathematical patterns in nature. As I understand it he modelled diffusion of antagonistic and ...

3

I currently work alongside many biologists that are working on simulations of anti-microbial peptides in the membrane. These seem to have a similar mechanism to what you're aiming for — permeating the lipid bilayer. Presumably you have already come to the conclusion that molecular dynamic simulations are probably a good shot for exploring what may ...

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