diff --git a/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch b/pkgs/by-name/cy/cytoscape/gen_vmoptions_to_homedir.patch
similarity index 100%
rename from pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch
rename to pkgs/by-name/cy/cytoscape/gen_vmoptions_to_homedir.patch
diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/by-name/cy/cytoscape/package.nix
similarity index 90%
rename from pkgs/applications/science/misc/cytoscape/default.nix
rename to pkgs/by-name/cy/cytoscape/package.nix
index 9be37db1b6d0..42b13f74000f 100644
--- a/pkgs/applications/science/misc/cytoscape/default.nix
+++ b/pkgs/by-name/cy/cytoscape/package.nix
@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchurl,
-  jre,
+  openjdk17,
   makeWrapper,
   replaceVars,
   coreutils,
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ jre ];
+  buildInputs = [ openjdk17 ];
 
   installPhase = ''
     mkdir -pv $out/{share,bin}
@@ -35,8 +35,8 @@ stdenv.mkDerivation rec {
     ln -s $out/share/cytoscape.sh $out/bin/cytoscape
 
     wrapProgram $out/share/cytoscape.sh \
-      --set JAVA_HOME "${jre}" \
-      --set JAVA  "${jre}/bin/java"
+      --set JAVA_HOME "${openjdk17}" \
+      --set JAVA  "${openjdk17}/bin/java"
 
     chmod +x $out/bin/cytoscape
   '';
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index a39f82402cec..dacc4a7d7ffd 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15250,10 +15250,6 @@ with pkgs;
 
   convertall = qt5.callPackage ../applications/science/misc/convertall { };
 
-  cytoscape = callPackage ../applications/science/misc/cytoscape {
-    jre = openjdk17;
-  };
-
   faissWithCuda = faiss.override {
     cudaSupport = true;
   };