text: user2004: Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them?
  What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.
  
  user48: To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have enough knowledge, time and computationally power to do this.
  At the moment I'm only aware of a paper simulating the Mycoplasma genitalium cell. But I'm not sure it was worth the effort as I haven't seen replicated or redone with other species, perhaps the model was not accurate enough to be worth it. 
  The tools used are here. The licenses are not a standard, but at least they seem free.
  
original_text: 2004: <p>Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a <a href="https://en.wikipedia.org/wiki/Flux_balance_analysis" rel="nofollow noreferrer">flux balance analysis</a> model out of them?</p>
  
  <p>What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.</p>
   48: <p>To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have enough knowledge, time and computationally power to do this.</p>
  
  <p>At the moment I'm only aware of a <a href="https://www.cell.com/abstract/S0092-8674%2812%2900776-3" rel="nofollow noreferrer">paper</a> simulating the <em>Mycoplasma genitalium</em> cell. But I'm not sure it was worth the effort as I haven't seen replicated or redone with other species, perhaps the model was not accurate enough to be worth it. </p>
  
  <p>The tools used are <a href="http://www.wholecell.org/" rel="nofollow noreferrer">here</a>. The licenses are not a standard, but at least they seem free.</p>
  