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8

kmm's answer is great and complete; I just want to add some of my points on what kind of data should follow Gaussian distribution. Unless you know from observation that a process doesn't follow a Gaussian distribution (e.g., Poisson, binomial, etc.), then it probably does at least well enough for statistical purposes. I won't fault kmm for this ...


8

You raise two issues, both of which might be better suited for stats.SE, but I think the questions are suitably biological to warrant an answer here. Do most biological processes follow a Gaussian distribution? Unless you know from observation that a process doesn't follow a Gaussian distribution (e.g., Poisson, binomial, etc.), then it probably does at ...


7

Cancer cells can be and are used in cell culture. HeLa cells were the first human cell line to be grown in culture and they were derived from a cervical tumor. That being said, Cancer cell lines would not necessarily be used for stem cell work. They have sustained too many mutations to study the type of questions that stem cells are used to study, though as ...


6

Adding onto AMR's answer, cancer cell lines are used extensively for research. They are typically fast to grow. HeLa Long grow to capacity of a 10cm dish within about 48hours, depending how you split them. Now some lines are different than others and each have their pros/cons but the main thing behind them is they make it possible to view the effects of ...


6

Is the standard Lotka-Volterra (LV) model an exact fit for insulin-glucose (IG) dynamics? No. Can a similar model built on the same principles capture most of the essential features of the IG dynamics? Absolutely. How to capture most of the insulin-glucose dynamics using a slightly modified Lotka-Volterra model We can figure out how to change the LV ...


6

The situation that you presented in which an entity A inhibits the production of another entity B which in turn inhibits A, is a positive feedback. In a network path or a loop the overall sign of the loop/path is the product of the signs of individual edges (interactions). In this case it is negative times negative which gives a positive sign to the loop. ...


5

Let's start with your definition. "Selection for traits that would be beneficial to a population of units at the expense of an individual unit possessing the trait" This is not a good definition of group selection. In reality, selection can act on groups regardless of the direction of selection at the individual level. This definition sounds to me (your ...


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 ...


4

Can we tell if a species will develop a specific character, based on the environment they're in? This is a major part of what quantitative genetics does. Or more detailedly, quantitative genetics can predict, for a population, changes in a trait given a selection pressure. First of all, for evolution to occur there must be variation in the trait you are ...


4

I'm afraid I laughed a bit when reading that paper for the first time. Why? Well, here's what they essentially did: They tried to model evolution by implementing an algorithm. They had a population of 10000 individuals, represented by their genetic sequence, and had an algorithm do mutations of those sequences and modeled selection and reproduction to get ...


4

The problem with increasingly complex HMMs is that their parameter space tends to explode with the nth-order of the HMMs. Higher number of parameters is often not great because it reduces the possible number of observations that go into training each parameter and can increase overfitting of the model. From the information that you are providing it is ...


4

First, Allee effects (also positive density dependence) can be modelled in several different ways, and the equation you give is one example. The terms weak and strong Allee effects are in my experience used in a couple of different ways. Most often, strong density dependence is used to denote Allee effects where the per capita population growth rate can ...


4

The Jacobian tells how the system changes along different state variables (which can be, for instance, the concentrations of the predator and the prey). The Jacobian matrix by itself doesn't give you a lot of intuitive information. However, the eigenvalues of the Jacobian matrix at the equilibrium point tell you the nature of the steady state. For example ...


3

Regarding your question about whether cancer cells could be used in studying stem cells: I have done stem cell work, and we used various teratoma cell lines (which are cancers that resemble germline tissue) in parallel with embryonic stem cells (ES cells) and induced pluripotent stem cells (iPS cells) for various experiments. Of course the choice of ...


3

John Harte's work on applying the mathematical theory of maximum entropy to ecology is certainly one of the better known examples of the application of this area of mathematics to science, in part because he literally wrote the textbook: Maximum Entropy and Ecology: A Theory of Abundance, Distribution, and Energetics (Oxford Series in Ecology and Evolution) ...


3

Since you are asking for the biological interpretations about these parameters, it is important to realize that the model you are presenting is a non-dimensionalized version of this model: $$ \frac{dx_1}{dt} =b_1x_1\Big(1- \Big(\frac{x_1 + \beta_{12}x_2}{K_1} \Big)\Big) $$ $$ \frac{dx_2}{dt} =b_2x_2\Big(1- \Big(\frac{x_2 + \beta_{21}x_1}{K_2} \Big)\Big), $$ ...


3

A Poisson process follows these postulates: $\lim\limits_{h\to0+}\frac{P(N_h=1)}h=\lambda$ i.e. the probability of occurrence one event in a very small interval of time is equal to the macroscopic rate or intensity ($\lambda\,$). $P(N_h\geqslant2)=o(h)$ i.e. the probability of occurrence of more than one events in an infinitesimal interval is essentially ...


3

Are kin selection and group selection the same thing? Yes and no. Yes: These days people tend to use the "direct fitness approach" (Taylor and Frank JTB 1996). It turns out that this is based on EXACTLY the same equation as is contextual analysis, which is the currently favored approach for measuring multilevel selection in natural populations (...


3

I figured it out, t' is just a dummy variable used to represent time over the refractory period since the integral is from t-r to t.


3

Theoretical ecology From wikipedia Theoretical ecology is the scientific discipline devoted to the study of ecological systems using theoretical methods such as simple conceptual models, mathematical models, computational simulations, and advanced data analysis. Effective models improve understanding of the natural world by revealing how the dynamics of ...


3

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

Roche's Biochemical Pathways works as a big png image and just put labels on the map. But you could try to extract data using queries like http://biochemical-pathways.com/pol/fts/query?query=Glutarate It seems to be legal as it's not prohibited.


3

Considering your assumption: I'm just looking at the exponential part, where the simple exponential equation works. If we assume there's sufficient nutrients for bacteria to grow unchecked for a number of hours (more-or-less true in a real culture) In your original model you are using discrete states and fixed time steps. So, if 30 min is one ...


2

NAMD is a molecular simulation software system with an extensive, active community of researchers https://www-s.ks.uiuc.edu/Research/namd/ it has a slick visualization package called VMD https://www-s.ks.uiuc.edu/Research/vmd/


2

Interpreting your question as "would the Lotka-Volterra predator-prey model be a good model for the glucose-insulin system?" my answer is "no". The predator-prey equations capture assumptions about how prey and predator interact with each other, and how they would fare on their own. These assumptions are not equivalent to any reasonable assumptions about the ...


2

Reiterating the above comments. Have a look at Tajima's D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model. The general form of the estimation for a diploid population is $E[S]=4N\mu\sum_{i=0}^{n-1} \frac{1}{i}$. Here the mutation rate of is per-genome not per-site, so $\mu=L * 10^{-9}$ where $L$ ...


2

The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that have different breeding systems, e.g. in Silene [1]. Past bottlenecks are also expected to decrease polymorphisms [2]. So, the answer to your question would ...


2

Your intuitions all seem correct. Coalescent simulation should be faster, because you don't track the entire population history over all t generations as you do in the forward simulation. Rather, as you work backwards in time you are tracking a smaller and small population. And with coalescent simulations it is probably very hard to incorporate the full ...


2

I've worked on a couple of these for biofuel production. The answer varies widely according to plant P and how well studied plant P is. In terms of what data is used, it includes but is not limited to: temperature, insolation, length of the day, cloud cover, rain, soil composition, soil type, soil density, other local effects like wind or pests, altitude, ...


2

From the way I have read what you have written z(1-z) translated into a sentence would be the frequency of the neutral variant (z) times the frequency of all other possible variants (1 - z) at the particular time t. Nucleotide diversity is then the average of 2 times the sum of all of the frequencies of neutral variants (z) times the the frequency of all ...



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