Don't use with.

Using with is an antipattern:

https://nix.dev/anti-patterns/language.html#with-attrset-expression

ginsim.nix

@@ -86,14 +86,12 @@ stdenv.mkDerivation rec {
     --set _JAVA_AWT_WM_NONREPARENTING 1
   '';
 
-  # Some easy metadata, in case I forget.  I use the with statement to
-  # avoid typing stdenv.lib to specify the license, the platform and
-  # the maintainer.
-  meta =  with stdenv.lib; {
+  # Some easy metadata, in case I forget.
+  meta = {
     homepage = "http://ginsim.org/";
     description = "A computer tool for the modeling and simulation of genetic regulatory networks.";
-    license = licenses.gpl3;
-    platforms = platforms.unix;
-    maintainers = [ maintainers.scolobb ];
+    license = stdenv.lib.licenses.gpl3;
+    platforms = stdenv.lib.platforms.unix;
+    maintainers = [ stdenv.lib.maintainers.scolobb ];
   };
 }

shell.nix

@@ -19,11 +19,12 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-
-# The with statement imports the nixpkgs namespace, so the tools like
-# stdenv and callPackage become available.
-with import <nixpkgs> {};
-stdenv.mkDerivation {
+# Import nixpkgs under the local binding pkgs to be able to use stdenv
+# and callPackage.
+let
+  pkgs = import <nixpkgs> {};
+in
+pkgs.stdenv.mkDerivation {
   name = "GINsim-shell";
 
   # Bring the package defined in ginsim.nix in scope.  buildInputs is
@@ -35,5 +36,5 @@ stdenv.mkDerivation {
   # callPackage can also be replaced by import.  In this case, the
   # arguments of the anonymous function defined in ginsim.nix get
   # their respective default values.
-  buildInputs = [ (callPackage ./ginsim.nix {}) ];
+  buildInputs = [ (pkgs.callPackage ./ginsim.nix {}) ];
 }