Hot answers tagged

73

Biological examples similar to programming statements: 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 ...


13

The answer is mostly no, and this is not as disruptive a statement as it seems to be. I think Brenner has a point of course and he is not the only one who wonders whether the systems biology can create a holistic model of living things. Still I wouldn't take this to mean we should stop doing systems biology research. At 18:30 brenner illustrates the ...


12

Systems Biology Wingreen & Botstein who run the graduate systems biology course at Princeton wrote a paper about how to teach the subject (Wingreen & Botstein, 2006). In the paper they highlight the key concepts they think are crucial to understanding modern systems biology, and they teach the course through discussion of seminal papers in the field....


12

There are certainly some comparisons that could be made between the way genes are expressed from DNA and logic functions, but they aren't great. But synthetic Biology is really a blossoming new field that is attempting to integrate logic functions into biology, see e.g. Siuti et al (2013). The above paper is a brilliant example of a group using using ...


9

Just to add to previous answers, but transcriptional interference (see e.g. Shearwin et al., 2005) can be seen as a form of IF-statement (or WHILE) in the sense that: if(x transcribed){not y transcribed} The interference does not have to be binary though, and more common are graded responses. Transcriptional interference can also take place at the RNA ...


6

DNA is not analogous to computer code which renders your search for similar constructs in it meaningless. To give a couple of simple examples why this is: Computer code has a sequential order of execution; DNA acts in parallel and out of sequence, it is not "executed". Computer code has a strict and consistent meaning so the line if x==4 : x=7 always does ...


6

The article is well known and discussed amongst systems biologists. It makes a good point - high throughput, observational biology cannot substitute for mechanistic studies that provide causal information. But we know an awful lot about biological systems already. All systems biologists are using information from the forward approach implicitly when they ...


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

I have a similar background (CS switching to systems biology) and I learned a great deal by reading "Systems Biology: A Textbook" by Edda Klipp et al [1]. It's a very good overview of different sub-areas and it's written in a way that's friendlier to a technical mind than most other bio-related books (i. e. concise, to the point, not shy with formulas). The ...


5

As WYSIWYG said there is no equivalent for function calls, as there will always be some interference. However one could argue that some modular pathways (eg. apoptosis signalling) can be seen as a "code block" where a certain input will (almost) certainly lead to a certain effect. The analogy with function calls is that, in describing many different ...


4

This phenomenon of being insensitive to certain fluctuations is called robustness. The fluctuations can be of two kinds for an input-output device such as a gene that is activated by a signal: Fluctuations in the signal Fluctuations in the intrinsic parameters Signal fluctuations can be temporal but parameter fluctuations are not (parameters are supposed ...


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

The model used by Jamshidi et al. can be found in the BioModels database with acession no. MODEL1103210001 http://www.ebi.ac.uk/compneur-srv/biomodels-main/MODEL1103210001 A more recent model has also been described in Bordbar et al. iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological ...


4

In your case, RNA expression and transcriptional activity probably differ in the stage of processing. Transcriptional activity refers to the binding and processive activity of RNA polymerase. There are different ways to measure this experimentally, but with a microarray you are measuring the amount of actual transcripts relative to the control array. RNA ...


4

For that you would need to understand the dynamical systems theory behind the loop. The point at which the oscillation starts is called the Hopf-bifurcation. I shall explain this in simple intuitive terms. Lets assume that Protein-X activates the production of Protein-Y which in-turn causes inhibition of Protein-X production. This is a negative feedback loop....


3

There is a recent published book, from Garland Science for systems biology http://www.garlandscience.com/product/isbn/9780815344674 and a clasic textbook: Physical Biology of the Cell http://www.garlandscience.com/product/isbn/9780815341635


3

Inferring transcriptional / regulatory networks from empirical data is an active area of research, and to my knowledge there aren't many mature tools for this type of analysis. I see mostly mathematicians, statisticians, and engineers working on this problem, probably because of the intense quantitative theory involved. Even if mature tools do exist, I doubt ...


3

You are right this is a typo. Equation 5 is just a restatement of the definition of the dot product of two vectors: $$\mathbf{u}_k^T\cdot \mathbf{x} = \sum_{i=1}^m u_{ki}^Tx_i$$ or written in another way $$\mathbf{u}_k^T\cdot \mathbf{x} = u_{k1}x_1+u_{k2}x_2+\cdots+u_{km}x_m.$$ In the text Equation 5 is stating that one can find a linear combination of the ...


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 ...


2

As far as I know, there is no one model officially known as "the Human Metabolic Model", but the Recon 2 model, described as a "consensus" model and the most comprehensive to date in Thiele et al. 2013, A community-driven global reconstruction of human metabolism (http://www.nature.com/nbt/journal/v31/n5/full/nbt.2488.html) is available at http://...


2

Firstly, it is important to remember that Flux Balance Analysis computes theoretical performance limits, i.e, the theoretically optimal behaviour of the system with respect to the objective and constraints. When growing bacterial cells growing in culture evolve under selection pressure for biomass production, the theoretical limit on biomass production may ...


2

Here there are a couple that I own: The "classic" from Uri Alon touches many of the topics you mention. It is easy to read and goes relatively deep into the methods. There seems to be a new edition (if you search it in Amazon it will pop up), but it was planned for last year's April and then delayed so no so clear when will be actually published. For the ...


2

It is common that reactions in stoichiometric models cannot carry flux because there is a "dead end" metabolite somewhere. The problem may not be in the immediate reactants / products, but can be several steps away, and is not always easy to find. If you have a network visualization tool, one option is to highlight all reactions that cannot carry flux; ...


2

Metabolism ≈ Anabolism + catabolism Metabolism is the set of all chemical reactions happening inside a living body. These reactions can either breaks down big molecules and build up big molecules. The set of reactions the breaks down big molecules is called catabolism. The set of reactions that build up big molecules is called anabolism. Energy Generally ...


1

The immune system recognizes patterns - incase of innate immunity and shapes - incase of active immunity. I am making a few assumptions: The Shrinking would result in a smaller version of "the person" - meaning he/she is a bacteria sized person capable of executing all actions that a human can do. The shrunk person is placed inside the blood vessel or ...


1

This is a very interesting question. As others have alluded to, the body generally recognises self and non-self. However, as with any biology it's not that simple. Even leaving aside autoimmune disorders, the body doesn't always attack non-self and doesn't always leave self alone. Think of a pregnancy - the foetus is non-self, and yet the body doesn't reject ...


1

Enzymes usualy have a relative narrow temperature optimum, for those of our body this is usually around 37°C. It is around 37,2°C in the morning and goes slightly up to 37,7°C in the evening (see reference 1 for details). The temparature optimum for most enzymes looks somewhat like displayed in the figure (from here, interesting to read): Enzymes are ...


1

If your data came from a single lab and a standard protocol gcrma normalisation is a good method to use (and comes with the affy R package); if the arrays are of U133A or HGU133plus2 types frozen RMA may be a good method to use. Finally you can check for and control for batch effects using ComBat and use the corrected expression data.


1

This is not an easy task, as there are many factors which you have to take in account. First there are intra-essay differences as slightly different conditions for each set of probes for the repetitions. Then, there are inter-assay differences, as differences in the array slides and so on, this paper ("Analysis of microarray gene expression data") goes into ...


1

NCBI BioSystems help file contains a list of their sources: http://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_help.html#SourceDatabases Please specify what you need as stated in the comments as it is almost impossible to give you more (relevant) information then this.



Only top voted, non community-wiki answers of a minimum length are eligible