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biosustain · Aug 5, 2015 · 5ee5821 · 5ee5821
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diff --git a/docs/1-quick-start.rst b/docs/1-quick-start.rst
diff --git a/docs/2-import-models.rst b/docs/2-import-models.rst
diff --git a/docs/3-simulate-models.rst b/docs/3-simulate-models.rst
@@ -6,11 +6,8 @@
     from cameo import load_model
     model = load_model("iJO1366")
 
-Simulating models with
-======================
-
-**c**\ omputer **a**\ ided **m**\ etabolic **e**\ ngineering and
-**o**\ ptimization
+Simulate models
+===============
 
 **cameo** uses and extends the model data structures defined by
 `cobrapy <https://opencobra.github.io/cobrapy/>`__, our favorite
@@ -72,17 +69,17 @@ Flux Balance Analysis
 ---------------------
 
 In **cameo**, flux balance analysis can be performed with the function
-``fba``.
+`fba`.
 
 .. code:: python
 
     from cameo import fba
     fba_result = fba(model)
 
-Basically, ``fba`` calls ``model.solve()`` and wraps the optimization
-solution in a ``FluxDistributionResult`` object. The maximum objective
+Basically, `fba` calls `model.solve()` and wraps the optimization
+solution in a `FluxDistributionResult` object. The maximum objective
 values (corresponding to a maximum growth rate) can obtained throug
-``result.objective_value``.
+`result.objective_value`.
 
 .. code:: python
 
@@ -120,14 +117,14 @@ low.
     ~ & ~ \mathbf{v}_{lb} \leq \mathbf{v} \leq \mathbf{v}_{ub} \,.
    \end{align}
 
-In **cameo**, pFBA can be performed with the function ``pfba``.
+In **cameo**, pFBA can be performed with the function `pfba`.
 
 .. code:: python
 
     from cameo import pfba
     pfba_result = pfba(model)
 
-The ``objective_function`` value is :math:`\lvert \mathbf{v} \rvert` ...
+The `objective_function` value is :math:`\lvert \mathbf{v} \rvert` ...
 
 .. code:: python
 

diff --git a/docs/4-analyze-models.rst b/docs/4-analyze-models.rst
diff --git a/docs/5-predict-expression-modulation-targets.rst b/docs/5-predict-expression-modulation-targets.rst
diff --git a/docs/6-predict-gene-knockout-strategies.rst b/docs/6-predict-gene-knockout-strategies.rst
diff --git a/docs/7-predict-heterologous-pathways.rst b/docs/7-predict-heterologous-pathways.rst
diff --git a/docs/8-high-level-API.rst b/docs/8-high-level-API.rst
diff --git a/docs/How_to.rst b/docs/How_to.rst
diff --git a/docs/Makefile b/docs/Makefile
@@ -49,6 +49,7 @@ help:
 
 ipy2rst:
 	for i in notebooks/*.ipynb; do ipython nbconvert $$i --to rst; done
+	sed -i '' 's/``/`/g' *.rst
 
 clean:
 	rm -rf $(BUILDDIR)/*

diff --git a/docs/Quickstart.ipynb b/docs/Quickstart.ipynb