Questions tagged [systems-biology]
An interdisciplinary area of study in the life sciences with a focus on complex interactions and large networks of biological molecules and processes.
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Performing Flux Balance Analysis (FBA) or Metabolic Flux Analysis (MFA) on tracer metabolomic data
I have targeted tracer metabolomic data of a mammalian cell culture in 3 biological replicates, and 3 time-points (0, 10 and 60 minutes). Cultures were fed with 13C6-glucose. After manual curation I ...
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what are the nodes and edges in gene regulatory networks
I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that
1)explain how one can get ...
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"Free space" volume in the nucleus
Take a mammalian cell, say a HeLa cell for concreteness. If a molecule (e.g. a transcription factor) enters the nucleus, what is the effective volume that it can explore/access there by free diffusion?...
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What does it mean to quantitatively describe a cell?
To begin this question, I will quote Molecular Biology of the Cell (page 38):
... Biological systems are, ..., full of feedback loops, and the behavior of even the simplest of systems with feedback ...
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Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?
I'm looking to phase-separate the expression of two enzymes and hence am looking for a multi-component genetic oscillator. However, repressilators and metabolators have a large period of around 45 ...
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How does species diversity vs Earth total biomass relate?
Are there any laws/theoretical foundations about how diversity of species relate with total biomass on Earth?
While there is a lot of esoteric sort of talk "humanity dis-balances the live on the ...
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Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?
I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins.
I would specifically be interested by a system biology ...
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Proteomics data Vs Transcriptomics data?
I want to use either of Proteomics or Transcriptomics data for integrating it into my kinetic model. Before proceeding, I want to know what are the advantages of using either of them so that I could ...
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How to integrate transcriptomics data with kinetic metabolic models?
I have created a convenience kinetics† model. Now, I want to integrate the transcriptomics data with my convenience kinetics model for altering/weighing the kinetic parameter values. I have ...
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Can GENESIS simulation software be adapted to other types of tissues?
GENESIS simulation software http://genesis-sim.org/ is designed for neurobiological systems and it is able to inculude in the simulation the different resolution levels - starting from the molecular ...
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What physiological processes give rise to a linear cell survival curve?
If we plot the number of surviving cells in a structure over time (assuming no replacement), the shape of that curve should imply something about the underlying process responsible for cell death. For ...
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Bistability vs bimodelity
In a systematic viewpoint, bistability refers to the existence of two stable equilibriums for a biological system. But, I don't understand the difference between bistability and bimodality. In both ...
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How interrelated are computational biology and biophysics? [closed]
I am considering applying to Ph.D. programs, and am not sure what direction to take. I'm hoping you all can help me out.
I have a background in both biology (molecular focus) and physics (condensed ...
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introduction of system biology to bench biologists [closed]
I am trained as a bench biologist and I want to learn about system biology and introduce a system biology type of analysis into my study. Can somebody recommend books and websites about system biology ...
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How to derive rate of product formation for an allosterically inhibited enzyme?
I'm working through Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls, and in Chapter 3 there's an example of a simple allosterically inhibited enzyme with reaction scheme ...
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Database of time lapse stem cell differentiation
Currently I am working on a project about modelling the social behaviours of embryonic stem cells (or induced pluripotent stem cells). I need a series of time-lapse live cell images which recording ...
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How to read from flow chart
So I got the following picture and question:
a) Assume that F1 = 10 mmol h$^{-1}$ and the flow is not negative (ie f$_i$ ≥ 0,
i = 1, ..., 8). What is the most you can produce of the polymer DCDE (i.e....
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Why is it desirable to couple chemical production to growth?
I have the following question in systems biology:
a) Draw a graph showing the relationship of growth (Vbio) and Vefni for the system here. (Let the horizontal axis represent Vbio and the vertical axis ...
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Can any systems biology model be complete?
In systems biology, models identify the primary actors in the body system, but can any model which does not include all secondary actors be said to be complete?
The current sysbio paradigm is to ...
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What motivation is there to create general, cross-species neural models which account for the variation between species in different environments?
The main components of human neuroanatomy have been mapped out. What attempt has there been to map a broad (many-species) spectrum of functional parts of the nervous system? Such a mapping could be ...
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Can a protein falling below a threshold trigger another response?
Is it possible that the falling of the concentration of a protein below a threshold triggers the release or production of another protein?
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FitzHugh–Nagumo system with diffusion
I was studying the FitzHugh-Nagumo model with diffusion and I quite do not understand the meaning of it.
If we consider the system without diffusion,
\begin{equation}\label{FHN}\begin{cases}
\dot{u}=...
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Is it possible to remove one strand of double stranded DNA in vivo?
Assume we do have a double stranded DNA sequence in human cells, say
...ATCGATATCGATATTGCAGAGCATAGCTATAA...
...TAGCTATAGCTATAAGCTCTCGTATCGATATT...
Now I want to ...
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Is "A" inhibiting "B" and vice-versa, a positive feedback loop?
If product A inhibits the expression of product B, and product B inhibits the expression of product A, is this a positive feedback loop?
My thinking was to consider the scenario that A starts off ...
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Barcode exchange between neighbouring cells
I am currently interested in equipping animal cells in a tissue with individual barcodes. These barcodes should get amplified in the cells (not to a cell degrading extent, of course), and also ...
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Difference between pulse coupling and diffusive coupling In biological oscillators
What are the differences between pulse coupling found among neuron cells and diffusive coupling found in cells that exhibit calcium waves?
Moreover, in both methods, is it a strict requirement that ...
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A good software for agent based modelling?
Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions ...
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does life make or break?
Ok, this question seems like it may be impossible to answer, but would be interesting to see if anyone has an idea.
Throughout the course of a human life, do we make more molecular bonds than we ...
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Negative feedback loop and oscillations
According to the textbook Alberts Molecular Biology of the Cell (5th ed., p. 902), negative feedback loops cause oscillations when they are long delayed. I just can't figure out why.
Except for that,...
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Metabolic control theory: proof of the summation theorem?
I'm looking for a rigorous proof of the summation theorem of metabolic control theory. The only sources I find are the original papers by Kacser and Burns 1973 and Heinrich and Rapoport 1974, both of ...
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how to solve gap reactions in genome scale metabolic reconstruction [closed]
I'm making a project about modeling of nannochloropsis metabolism. My model is in the refinement stage. However, it is not running in the FBA test. Then i found there are 87 reactions that did not run....
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Critical discussion: Gene expression and systems biology allows us to understand the control of complex traits
I'm having a bit of trouble tackling this question. Any help on what I should write about or the points I should mention would be much appreciated. I keep seeing articles about eQTL and QTL are these ...
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System biology and evolution: Book-recommendations
I have relatively good knowledge in evolutionary biology and in population genetics. I am getting more and more interested in the evolution of ...
genetic developmental processes
gene interactions
...
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How does cancer of the larynx (laryngeal cancer) affect the respiratory system?
The larynx is part of the respiratory system and is responsible for producing sound (our voices). My question is how cancer in the larynx (voice box) affect the respiratory system overall? I ...
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What network motifs or other mechanisms can make the expression of a gene invariable to the environment?
Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?
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Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?
Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops?
In software development, these constructs have the following functions:
IF-statements: An IF statement executes the code in a ...
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Can your immune system's cells destroy you? (Critical thinking and Fictional sense)
In an imaginary sense, If you alone were replicated into 2 so that there should now be 2 of "you" (meaning you both have the same DNA). Then let's say one of you shrunk to the size of a bacteria, and ...
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Why the name coined for MARKUP LANGUAGE for SBML? [closed]
I'm get the confusion about SYSTEM BIOLOGY filed. SBML is refer to as SYSTEM BIOLOGY MARKUP LANGUAGE why we should called as <...
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Is the activity of enzymes in the human body affected by the outer temperature?
I have to do a research about the enzymes in the human body and the things that affect them. I know that the body temperature affects the activity of enzyemes but I'd like to know if the outer ...
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Valid comparison of gene expression between several genes in several cell lines
We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes. Our goal would be to be able to compare relative gene expression for genes over the ...
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Databases for metabolic pathways of human disease
Which databases contain the metabolic pathway of human diseases?
I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.
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Systems Biology of triacylglycerol (TAG) synthesis in Jatropha
I need the genetic regulatory network of TAG synthesis (Kennedy pathway) of Jatropha plant??
Or is there any way to convert metabolic pathway into genetic regulatory network?
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What are good data on the Human Metabolic Model and where can I get them?
Trying to get a good SBML representation of the Human Metabolic Model for use in Flux Balance Analysis and drug targetting (i.e. gene knockout) simulations.
What are good sources for these data?
...
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How usable is the Human Metabolic Model to predict biomass?
In order to use the Human Metabolic Model for Flux Balance Analysis of specific cancer cell lines, we would like to know what sort of flux values have been determined for the Human Metabolic Model.
...
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Where can I find the metabolic network for the human erythrocyte?
Where can I find the metabolic network of the human erythrocyte (red blood cell), in SBML format? The red blood cell metabolic network is a model that's usually employed in the literature [see refs ...
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Does this equation have a typo? (Systems Biology, singular value decomposition) [closed]
I'm reading a systems biology paper, and I'm suspecting there's a typo in an equation, but I want to make sure.
The article is "Systemic metabolic reactions are obtained by singular value ...
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How to relate human metabolic model reactions and cancer drug targets / reactome items?
Trying to find a way to take a cancer drug (from CancerDR, for instance) and infer the metabolic reactions that are affected by it in the Human Metabolic Model.
Essentially, I would like to know ...
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Statistics on energy consumption breakdown per biological functions across organisms?
Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of "Bacteria spend X% of energy on information processing, Y% for ...
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Recent and good quality articles on systems biology [closed]
I'm a biotechnology student and I have to write a sort of non-experimental thesis (30 pages long) within the end of a three years study.
I'm very interested in the "systems biology" field and I'm ...
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Difference between "transcriptional activity" and "RNA expression"
I am working with a network object where the nodes are different events in molecular biology.
Specifically;
Catalytic activity of X,
RNA expression of X,
GTP-bound activity of X,
Kinase activity of X,...
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