bsys-eval is a tool meant to help study the likelihood of a given scenario in a biological system.
Given a set of target species, a set of constraints on the target species (constraints which model a scenario that could present, for example, in a disease) and by taking into account all the reactions that lead to the production, both directly and indirectly, of the target species, the goal is to find a subset of virtual patients for the situation.
High Concentration Molecules
Estrogen: A steroid hormone that freely diffuses across cell membranes Calcium ions (Ca²⁺): Present in high concentrations within cellular compartments, particularly important for amplifying signals β-Actin: A structural protein maintaining high concentrations as part of the cytoskeletal framework
Low Concentration Molecules
Dopamine: A neurotransmitter present in very low concentrations but highly effective in signaling Epidermal Growth Factor (EGF): A growth factor typically found in trace amounts due to its potent effects HER2: A signaling protein that requires minimal amounts for effective signaling
input: { 29356, 29364, 29368, 29468, 5693375, 1497830, 164358, 5610577, 5610579
output: { 70106, 29968, 29336, 202124
In the context of signal transduction pathways, species can refer to various molecules such as proteins, ions, or other signaling molecules. Here are two sets based on their concentration levels:
- High Concentration Species
- Cyclic AMP (cAMP) - A common second messenger that is often present in relatively high concentrations in cells.
- Calcium ions (Ca²⁺) - These ions are crucial for many signaling processes and can be found at high concentrations within specific compartments of the cell.
- Low Concentration Species
- Nitric Oxide (NO) - A signaling molecule that is typically present in very low concentrations due to its short half-life.
- Receptor Tyrosine Kinases (RTKs) - While these proteins are critical for signaling, their expression levels can vary widely, and they are often present at lower concentrations compared to other signaling molecules.
These sets illustrate the diversity in concentration levels of different species involved in signal transduction pathways