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12

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 ...


10

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 ...


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 ...


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 ...


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, ...


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 ...


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 ...


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 ...


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 ...


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.


1

Triacylglycerol synthesis in plants is probably highly conserved. The metabolic pathway is here. The Jatropha genome sequence is also available. Given this some effort has been made to figure out how these genes are regulated. This is a microarray study of Jatropha focusing on fatty acid and TAG biosynthesis. This gives some idea of how TAG genes ...


1

Short answer: For drugs with targets having a direct effect on reactions in the model: Find the gene name for the target protein -> Find the Entrez Gene ID (or other gene identifier, depending on the model) -> Search the model file or database for reactions having a gene association with the gene identifier. AND/OR: Find the EC number for the target ...


1

This question is extremely vague, and can't have any real answer without you specifying a question or at least focus. Keep in mind, there is no high-road to research, you will have to dig in and start reading papers to gain understanding of your field. If you want help from others, you should at least take time to list the papers that you have already read ...


1

I've been working to prepare a synthetic biology curriculum for non-biologist and have found a great resource in Prof. Scott Mohr's (BU, Chemistry) "Primer for Synthetic Biology" available here: http://openwetware.org/images/3/3d/SB_Primer_100707.pdf


1

I'd like to add regulonDB which is not as integrated, but has a tremendous map of the e coli regulome which would be useful for any bacterial model. I agree with @DanielStandage that this is not a well understood and there don't even appear to be standard representations for this sort of data.



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