diff --git a/.github/workflows/node.js.yml b/.github/workflows/node.js.yml
new file mode 100644
index 00000000..95e7af34
--- /dev/null
+++ b/.github/workflows/node.js.yml
@@ -0,0 +1,35 @@
+# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
+
+name: Node.js CI
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x, 22.x]
+
+    steps:
+    - uses: actions/checkout@v4
+    # install system dependencies needed by the 'canvas' package
+    - name: Install dependencies for canvas
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libcairo2-dev libpango1.0-dev libjpeg62 libgif-dev librsvg2-dev
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: 'npm'
+        
+    - run: npm ci
+    - run: npm run lint 
+    - run: npm run build --if-present
+    - run: npm test
+
+    
\ No newline at end of file
diff --git a/README.md b/README.md
index 0691c9c1..55ab02da 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,7 @@ GRNsight
 [![DOI](https://zenodo.org/badge/16195791.svg)](https://zenodo.org/badge/latestdoi/16195791)
 [![Build Status](https://app.travis-ci.com/dondi/GRNsight.svg?branch=master)](https://app.travis-ci.com/dondi/GRNsight)
 [![Coverage Status](https://coveralls.io/repos/github/dondi/GRNsight/badge.svg?branch=master)](https://coveralls.io/github/dondi/GRNsight?branch=master)
+[![Node.js CI](https://github.com/dondi/GRNsight/actions/workflows/node.js.yml/badge.svg)](https://github.com/dondi/GRNsight/actions/workflows/node.js.yml)
 
 http://dondi.github.io/GRNsight/
 
diff --git a/database/network-database/schema.sql b/database/network-database/schema.sql
index 59a315ff..377f845b 100644
--- a/database/network-database/schema.sql
+++ b/database/network-database/schema.sql
@@ -20,6 +20,6 @@ CREATE TABLE gene_regulatory_network.network (
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
   FOREIGN KEY (regulator_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
-  FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network_testing.gene(gene_id, taxon_id),
-  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network_testing.source(time_stamp, source)
+  FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
+  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source)
 ); 
\ No newline at end of file
diff --git a/database/protein-protein-database/schema.sql b/database/protein-protein-database/schema.sql
index 922bfac2..a2f43a94 100644
--- a/database/protein-protein-database/schema.sql
+++ b/database/protein-protein-database/schema.sql
@@ -20,7 +20,7 @@ CREATE TABLE protein_protein_interactions.protein (
   molecular_weight FLOAT,
   PI FLOAT,
   taxon_id VARCHAR,
-  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions_testing.gene(gene_id, taxon_id)
+  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions.gene(gene_id, taxon_id)
 );
 
 CREATE TABLE protein_protein_interactions.physical_interactions (
@@ -30,8 +30,8 @@ CREATE TABLE protein_protein_interactions.physical_interactions (
   experiment_name VARCHAR,
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
-  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions_testing.protein(standard_name),
-  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions_testing.protein(standard_name),
-  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions_testing.source(time_stamp, source),
+  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions.protein(standard_name),
+  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions.protein(standard_name),
+  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source),
   CONSTRAINT unique_physical_interaction UNIQUE (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source)
 );
diff --git a/package-lock.json b/package-lock.json
index bebb0710..b03f6255 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,16 +1,17 @@
 {
   "name": "grnsight",
-  "version": "6.0.0",
+  "version": "7.1.9",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "grnsight",
-      "version": "6.0.0",
+      "version": "7.1.9",
       "license": "BSD-3-Clause",
       "dependencies": {
         "body-parser": "1.18.2",
-        "canvg": "2.0.0",
+        "canvas": "^2.11.2",
+        "canvg": "3.0.10",
         "cors": "2.8.1",
         "cytoscape": "2.7.14",
         "d3-v4-grid": "2.0.1",
@@ -28,7 +29,7 @@
         "node-xlsx": "0.7.2",
         "nodemon": "1.19.1",
         "parallelshell": "3.0.1",
-        "pg": "8.0.0",
+        "pg": "8.0.3",
         "pg-hstore": "2.3.3",
         "pug": "3.0.2",
         "querystring": "0.2.0",
@@ -114,6 +115,22 @@
         "node": ">=6.0.0"
       }
     },
+    "node_modules/@babel/runtime": {
+      "version": "7.26.0",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.26.0.tgz",
+      "integrity": "sha512-FDSOghenHTiToteC/QRlv2q3DhPZ/oOXTBoirfWNx1Cx3TMVcGWQtMMmQcSvb/JjpNeGzx8Pq/b4fKEJuWm1sw==",
+      "dependencies": {
+        "regenerator-runtime": "^0.14.0"
+      },
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
+    "node_modules/@babel/runtime/node_modules/regenerator-runtime": {
+      "version": "0.14.1",
+      "resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.14.1.tgz",
+      "integrity": "sha512-dYnhHh0nJoMfnkZs6GmmhFknAGRrLznOu5nc9ML+EJxGvrx6H7teuevqVqCuPcPK//3eDrrjQhehXVx9cnkGdw=="
+    },
     "node_modules/@babel/types": {
       "version": "7.16.0",
       "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.16.0.tgz",
@@ -127,15 +144,14 @@
       }
     },
     "node_modules/@mapbox/node-pre-gyp": {
-      "version": "1.0.8",
-      "resolved": "https://registry.npmjs.org/@mapbox/node-pre-gyp/-/node-pre-gyp-1.0.8.tgz",
-      "integrity": "sha512-CMGKi28CF+qlbXh26hDe6NxCd7amqeAzEqnS6IHeO6LoaKyM/n+Xw3HT1COdq8cuioOdlKdqn/hCmqPUOMOywg==",
-      "peer": true,
+      "version": "1.0.11",
+      "resolved": "https://registry.npmjs.org/@mapbox/node-pre-gyp/-/node-pre-gyp-1.0.11.tgz",
+      "integrity": "sha512-Yhlar6v9WQgUp/He7BdgzOz8lqMQ8sU+jkCq7Wx8Myc5YFJLbEe7lgui/V7G1qB1DJykHSGwreceSaD60Y0PUQ==",
       "dependencies": {
-        "detect-libc": "^1.0.3",
+        "detect-libc": "^2.0.0",
         "https-proxy-agent": "^5.0.0",
         "make-dir": "^3.1.0",
-        "node-fetch": "^2.6.5",
+        "node-fetch": "^2.6.7",
         "nopt": "^5.0.0",
         "npmlog": "^5.0.1",
         "rimraf": "^3.0.2",
@@ -146,23 +162,10 @@
         "node-pre-gyp": "bin/node-pre-gyp"
       }
     },
-    "node_modules/@mapbox/node-pre-gyp/node_modules/lru-cache": {
-      "version": "6.0.0",
-      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-6.0.0.tgz",
-      "integrity": "sha512-Jo6dJ04CmSjuznwJSS3pUeWmd/H0ffTlkXXgwZi+eq1UCmqQwCh+eLsYOYCwY991i2Fah4h1BEMCx4qThGbsiA==",
-      "peer": true,
-      "dependencies": {
-        "yallist": "^4.0.0"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/@mapbox/node-pre-gyp/node_modules/make-dir": {
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/make-dir/-/make-dir-3.1.0.tgz",
       "integrity": "sha512-g3FeP20LNwhALb/6Cz6Dd4F2ngze0jz7tbzrD2wAV+o9FeNHe4rL+yK2md0J/fiSf1sa1ADhXqi5+oVwOM/eGw==",
-      "peer": true,
       "dependencies": {
         "semver": "^6.0.0"
       },
@@ -174,19 +177,17 @@
       }
     },
     "node_modules/@mapbox/node-pre-gyp/node_modules/make-dir/node_modules/semver": {
-      "version": "6.3.0",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz",
-      "integrity": "sha512-b39TBaTSfV6yBrapU89p5fKekE2m/NwnDocOVruQFS1/veMgdzuPcnOM34M6CwxW8jH/lxEa5rBoDeUwu5HHTw==",
-      "peer": true,
+      "version": "6.3.1",
+      "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.1.tgz",
+      "integrity": "sha512-BR7VvDCVHO+q2xBEWskxS6DJE1qRnb7DxzUrogb71CWoSficBxYsiAGd+Kl0mmq/MprG9yArRkyrQxTO6XjMzA==",
       "bin": {
         "semver": "bin/semver.js"
       }
     },
     "node_modules/@mapbox/node-pre-gyp/node_modules/node-fetch": {
-      "version": "2.6.7",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
-      "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==",
-      "peer": true,
+      "version": "2.7.0",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.7.0.tgz",
+      "integrity": "sha512-c4FRfUm/dbcWZ7U+1Wq0AwCyFL+3nt2bEw05wfxSz+DWpWsitgmSgYmy2dQdWyKC1694ELPqMs/YzUSNozLt8A==",
       "dependencies": {
         "whatwg-url": "^5.0.0"
       },
@@ -206,7 +207,6 @@
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/nopt/-/nopt-5.0.0.tgz",
       "integrity": "sha512-Tbj67rffqceeLpcRXrT7vKAN8CwfPeIBgM7E6iBkmKLV7bEMwpGgYLGv0jACUsECaa/vuxP0IjEont6umdMgtQ==",
-      "peer": true,
       "dependencies": {
         "abbrev": "1"
       },
@@ -221,7 +221,7 @@
       "version": "3.0.2",
       "resolved": "https://registry.npmjs.org/rimraf/-/rimraf-3.0.2.tgz",
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-      "peer": true,
+      "deprecated": "Rimraf versions prior to v4 are no longer supported",
       "dependencies": {
         "glob": "^7.1.3"
       },
@@ -233,13 +233,9 @@
       }
     },
     "node_modules/@mapbox/node-pre-gyp/node_modules/semver": {
-      "version": "7.3.5",
-      "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.5.tgz",
-      "integrity": "sha512-PoeGJYh8HK4BTO/a9Tf6ZG3veo/A7ZVsYrSA6J8ny9nb3B1VrpkuN+z9OE5wfE5p6H4LchYZsegiQgbJD94ZFQ==",
-      "peer": true,
-      "dependencies": {
-        "lru-cache": "^6.0.0"
-      },
+      "version": "7.6.3",
+      "resolved": "https://registry.npmjs.org/semver/-/semver-7.6.3.tgz",
+      "integrity": "sha512-oVekP1cKtI+CTDvHWYFUcMtsK/00wmAEfyqKfNdARm8u1wNVhSgaX7A8d4UuIlUI5e84iEwOhs7ZPYRmzU9U6A==",
       "bin": {
         "semver": "bin/semver.js"
       },
@@ -250,19 +246,12 @@
     "node_modules/@mapbox/node-pre-gyp/node_modules/whatwg-url": {
       "version": "5.0.0",
       "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
-      "integrity": "sha1-lmRU6HZUYuN2RNNib2dCzotwll0=",
-      "peer": true,
+      "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
       "dependencies": {
         "tr46": "~0.0.3",
         "webidl-conversions": "^3.0.0"
       }
     },
-    "node_modules/@mapbox/node-pre-gyp/node_modules/yallist": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
-      "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
-      "peer": true
-    },
     "node_modules/@mrmlnc/readdir-enhanced": {
       "version": "2.2.1",
       "resolved": "https://registry.npmjs.org/@mrmlnc/readdir-enhanced/-/readdir-enhanced-2.2.1.tgz",
@@ -356,6 +345,11 @@
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       "dev": true
     },
+    "node_modules/@types/raf": {
+      "version": "3.4.3",
+      "resolved": "https://registry.npmjs.org/@types/raf/-/raf-3.4.3.tgz",
+      "integrity": "sha512-c4YAvMedbPZ5tEyxzQdMoOhhJ4RD3rngZIdwC2/qDN3d7JpEhB6fiBRKVY1lg5B7Wk+uPBjn5f39j1/2MY1oOw=="
+    },
     "node_modules/abab": {
       "version": "1.0.4",
       "resolved": "https://registry.npmjs.org/abab/-/abab-1.0.4.tgz",
@@ -441,6 +435,7 @@
       "version": "6.2.0",
       "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-6.2.0.tgz",
       "integrity": "sha512-7evsyfH1cLOCdAzZAd43Cic04yKydNx0cF+7tiA19p1XnLLPU4dpCQOqpjqwokFe//vS0QqfqqjCS2JkiIs0cA==",
+      "dev": true,
       "engines": {
         "node": ">=0.4.0"
       }
@@ -460,7 +455,6 @@
       "version": "6.0.2",
       "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz",
       "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==",
-      "peer": true,
       "dependencies": {
         "debug": "4"
       },
@@ -469,12 +463,11 @@
       }
     },
     "node_modules/agent-base/node_modules/debug": {
-      "version": "4.3.3",
-      "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.3.tgz",
-      "integrity": "sha512-/zxw5+vh1Tfv+4Qn7a5nsbcJKPaSvCDhojn6FEl9vupwK2VCSDtEiEtqr8DFtzYFOdz63LBkxec7DYuc2jon6Q==",
-      "peer": true,
+      "version": "4.3.7",
+      "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.7.tgz",
+      "integrity": "sha512-Er2nc/H7RrMXZBFCEim6TCmMk02Z8vLC2Rbi1KEBggpo0fS6l0S1nnapwmIi3yW/+GOJap1Krg4w0Hg80oCqgQ==",
       "dependencies": {
-        "ms": "2.1.2"
+        "ms": "^2.1.3"
       },
       "engines": {
         "node": ">=6.0"
@@ -486,10 +479,9 @@
       }
     },
     "node_modules/agent-base/node_modules/ms": {
-      "version": "2.1.2",
-      "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz",
-      "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==",
-      "peer": true
+      "version": "2.1.3",
+      "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
+      "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA=="
     },
     "node_modules/ajv": {
       "version": "6.12.6",
@@ -601,7 +593,7 @@
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-2.0.0.tgz",
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-      "peer": true,
+      "deprecated": "This package is no longer supported.",
       "dependencies": {
         "delegates": "^1.0.0",
         "readable-stream": "^3.6.0"
@@ -611,10 +603,9 @@
       }
     },
     "node_modules/are-we-there-yet/node_modules/readable-stream": {
-      "version": "3.6.0",
-      "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-3.6.0.tgz",
-      "integrity": "sha512-BViHy7LKeTz4oNnkcLJ+lVSL6vpiFeX6/d3oSH8zCW7UxP2onchk+vTGB143xuFjHS3deTgkKoXXymXqymiIdA==",
-      "peer": true,
+      "version": "3.6.2",
+      "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-3.6.2.tgz",
+      "integrity": "sha512-9u/sniCrY3D5WdsERHzHE4G2YCXqoG5FTHUiCC4SIbr6XcLZBY05ya9EKjYek9O5xOAwjGq+1JdGBAS7Q9ScoA==",
       "dependencies": {
         "inherits": "^2.0.3",
         "string_decoder": "^1.1.1",
@@ -641,14 +632,12 @@
           "type": "consulting",
           "url": "https://feross.org/support"
         }
-      ],
-      "peer": true
+      ]
     },
     "node_modules/are-we-there-yet/node_modules/string_decoder": {
       "version": "1.3.0",
       "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz",
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-      "peer": true,
       "dependencies": {
         "safe-buffer": "~5.2.0"
       }
@@ -860,7 +849,8 @@
     "node_modules/async-limiter": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/async-limiter/-/async-limiter-1.0.1.tgz",
-      "integrity": "sha512-csOlWGAcRFJaI6m+F2WKdnMKr4HhdhFVBk0H/QbJFMCr+uO2kwohwXQPxw/9OCxp05r5ghVBFSyioixx3gfkNQ=="
+      "integrity": "sha512-csOlWGAcRFJaI6m+F2WKdnMKr4HhdhFVBk0H/QbJFMCr+uO2kwohwXQPxw/9OCxp05r5ghVBFSyioixx3gfkNQ==",
+      "dev": true
     },
     "node_modules/asynckit": {
       "version": "0.4.0",
@@ -2170,7 +2160,8 @@
     "node_modules/browser-process-hrtime": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/browser-process-hrtime/-/browser-process-hrtime-1.0.0.tgz",
-      "integrity": "sha512-9o5UecI3GhkpM6DrXr69PblIuWxPKk9Y0jHBRhdocZ2y7YECBFCsHm79Pr3OyR2AvjhDkabFJaDJMYRazHgsow=="
+      "integrity": "sha512-9o5UecI3GhkpM6DrXr69PblIuWxPKk9Y0jHBRhdocZ2y7YECBFCsHm79Pr3OyR2AvjhDkabFJaDJMYRazHgsow==",
+      "dev": true
     },
     "node_modules/browserify-aes": {
       "version": "1.2.0",
@@ -2519,14 +2510,13 @@
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-      "resolved": "https://registry.npmjs.org/canvas/-/canvas-2.9.0.tgz",
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+      "version": "2.11.2",
+      "resolved": "https://registry.npmjs.org/canvas/-/canvas-2.11.2.tgz",
+      "integrity": "sha512-ItanGBMrmRV7Py2Z+Xhs7cT+FNt5K0vPL4p9EZ/UX/Mu7hFbkxSjKF2KVtPwX7UYWp7dRKnrTvReflgrItJbdw==",
       "hasInstallScript": true,
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       "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz",
-      "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw=="
+      "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==",
+      "dev": true
     },
     "xmldom": {
       "version": "0.1.31",
diff --git a/package.json b/package.json
index c4c5708e..6675de48 100644
--- a/package.json
+++ b/package.json
@@ -1,13 +1,14 @@
 {
   "name": "grnsight",
-  "version": "7.1.2",
+  "version": "7.1.11",
   "description": "Web app and service for visualizing models of gene regulatory networks",
   "directories": {
     "test": "test"
   },
   "dependencies": {
     "body-parser": "1.18.2",
-    "canvg": "2.0.0",
+    "canvas": "^2.11.2",
+    "canvg": "3.0.10",
     "cors": "2.8.1",
     "cytoscape": "2.7.14",
     "d3-v4-grid": "2.0.1",
diff --git a/server/controllers/demo-workbooks.js b/server/controllers/demo-workbooks.js
index 3bdc0536..b18d0301 100644
--- a/server/controllers/demo-workbooks.js
+++ b/server/controllers/demo-workbooks.js
@@ -515,7 +515,7 @@ var demoWorkbook1 = function (path, res, app) {
         },
         meta: {
             data: {
-                alpha: 0.002,
+                alpha: 0.02,
                 kk_max: 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
@@ -2679,7 +2679,7 @@ var demoWorkbook2 = function (path, res, app) {
         },
         meta: {
             data: {
-                alpha: 0.002,
+                alpha: 0.02,
                 kk_max: 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
diff --git a/server/controllers/importers/sif.js b/server/controllers/importers/sif.js
index 34acbfad..ec4e996d 100644
--- a/server/controllers/importers/sif.js
+++ b/server/controllers/importers/sif.js
@@ -61,14 +61,15 @@ module.exports = function (sif) {
         if (allNumbers) {
             workbookType = constants.NETWORK_GRN_MODE;
         } else {
-            for (const relationship of relationships) {
-                if (relationship === "pp") {
-                    workbookType = constants.NETWORK_PPI_MODE;
-                    break;
-                } else if (relationship === "pd") {
-                    workbookType = constants.NETWORK_GRN_MODE;
-                    break;
-                }
+            let stringRelationships = relationships.filter(function (relationship) {
+                return !isNumber(relationship);
+            });
+            if (stringRelationships.every(rel => rel === "pp")) {
+                workbookType = constants.NETWORK_PPI_MODE;
+            } else if (stringRelationships.every(rel => rel === "pd")) {
+                workbookType = constants.NETWORK_GRN_MODE;
+            } else if (stringRelationships.every(rel => rel === "pp" || rel === "pd")) {
+                errors.push(sifConstants.errors.SIF_MIXED_RELATIONSHIP_TYPE_ERROR);
             }
         }
 
diff --git a/server/controllers/sif-constants.js b/server/controllers/sif-constants.js
index eedf9e87..0b9d9b42 100644
--- a/server/controllers/sif-constants.js
+++ b/server/controllers/sif-constants.js
@@ -32,5 +32,12 @@ module.exports = {
             possibleCause: "GRNsight has detected stray data and/or extraneous blank rows in your SIF file. ",
             suggestedFix: "Please review the data and delete extraneous data from the file."
         },
+
+        SIF_MIXED_RELATIONSHIP_TYPE_ERROR: {
+            errorCode: "SIF_MIXED_RELATIONSHIP_TYPE_ERROR",
+            possibleCause: "The SIF importer detects a SIF file with mixed relationship types.",
+            suggestedFix: ["GRNsight only supports networks with a single relationship type.",
+                "Please review the relationships for consistency."].join(" ")
+        },
     },
 };
diff --git a/server/dals/expression-dal.js b/server/dals/expression-dal.js
index 883a435a..11084515 100644
--- a/server/dals/expression-dal.js
+++ b/server/dals/expression-dal.js
@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
@@ -20,7 +20,7 @@ var sequelize = new Sequelize(
 const buildExpressionGenesQuery = function (geneString) {
     let genes = "";
     let geneList = geneString.split(",");
-    geneList.forEach(x => genes += ( `(gene_expression.gene.display_gene_id =\'${x}\') OR `));
+    geneList.forEach(x => genes += ( `(LOWER(gene_expression.gene.display_gene_id) = LOWER(\'${x}\')) OR `));
     return genes.substring(0, genes.length - 4);
 };
 
@@ -62,7 +62,7 @@ const buildExpressionQuery = function (query) {
 const listExpressionGeneData = function (gene, totalOutput) {
     let listOfData = [];
     totalOutput.forEach(function (x) {
-        if (x.display_gene_id === gene) {
+        if (x.display_gene_id.toLowerCase() === gene.toLowerCase()) {
             listOfData.push(Number(x.expression));
         }
     });
diff --git a/server/dals/grnsetting-dal.js b/server/dals/grnsetting-dal.js
index 2a19cdda..a5f67f75 100644
--- a/server/dals/grnsetting-dal.js
+++ b/server/dals/grnsetting-dal.js
@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
diff --git a/server/dals/network-dal.js b/server/dals/network-dal.js
index 0f53c713..65665655 100644
--- a/server/dals/network-dal.js
+++ b/server/dals/network-dal.js
@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
@@ -21,12 +21,10 @@ const buildNetworkSourceQuery = function () {
     return "SELECT * FROM gene_regulatory_network.source ORDER BY time_stamp DESC;";
 };
 
-const buildNetworkGeneFromSourceQuery = function (gene, source, timestamp) {
+const buildNetworkGeneFromSourceQuery = function (gene) {
     return `SELECT DISTINCT gene_id, display_gene_id FROM 
-    gene_regulatory_network.network, gene_regulatory_network.gene WHERE
-    network.time_stamp='${timestamp}' AND network.source='${source}' AND
-    (gene.gene_id ='${gene}' OR gene.display_gene_id ='${gene}') AND
-    (gene.gene_id = network.regulator_gene_id OR gene.gene_id = network.target_gene_id);`;
+    gene_regulatory_network.gene WHERE (gene.gene_id ='${gene}'
+    OR gene.display_gene_id ='${gene}')`;
 };
 
 const buildNetworkGenesQuery = function (geneString) {
@@ -49,7 +47,7 @@ const buildGenerateNetworkQuery = function (genes, source, timestamp) {
 const buildQueryByType = function (queryType, query) {
     const networkQueries = {
         "NetworkSource": () => buildNetworkSourceQuery(),
-        "NetworkGeneFromSource": () => buildNetworkGeneFromSourceQuery(query.gene, query.source, query.timestamp),
+        "NetworkGeneFromSource": () => buildNetworkGeneFromSourceQuery(query.gene),
         "GenerateNetwork": () => buildGenerateNetworkQuery(query.genes, query.source, query.timestamp)
     };
     if (Object.keys(networkQueries).includes(query.type)) {
diff --git a/server/dals/protein-dal.js b/server/dals/protein-dal.js
index bfd8dd3e..47127b21 100644
--- a/server/dals/protein-dal.js
+++ b/server/dals/protein-dal.js
@@ -4,8 +4,8 @@ var env = process.env.NODE_ENV || "development";
 var config = require("../config/config")[env];
 var sequelize = new Sequelize(
     config.databaseName,
-    process.env.EXPRESSION_DB_USERNAME,
-    process.env.EXPRESSION_DB_PASSWORD,
+    process.env.DB_USERNAME,
+    process.env.DB_PASSWORD,
     {
         host: config.databaseHost,
         dialect: config.databaseDialect,
diff --git a/test/additional-sheet-parser-tests.js b/test/additional-sheet-parser-tests.js
index 4566a1fa..8c41d1f1 100644
--- a/test/additional-sheet-parser-tests.js
+++ b/test/additional-sheet-parser-tests.js
@@ -62,7 +62,7 @@ describe("additional-sheet-parser", function () {
             var data = parseAdditionalSheets(workbook);
             /* eslint-disable */
             assert(data.meta, {
-                alpha: 0.002,
+                alpha: 0.02,
                 kk_max: 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
diff --git a/test/import-sif-tests.js b/test/import-sif-tests.js
index c0aea2e9..818c93b6 100644
--- a/test/import-sif-tests.js
+++ b/test/import-sif-tests.js
@@ -316,6 +316,13 @@ var sifWithSemanticErrorOnly = [
     "E"
 ].join("\r\n");
 
+var sifWithMixedRelationshipTypes = [
+    [ "A", "pd", "A" ].join("\t"),
+    [ "B", "pd", "A", "C" ].join("\t"),
+    [ "C", "pd", "B" ].join("\t"),
+    [ "D", "pp", "D" ].join("\t"),
+].join("\r\n");
+
 describe("Import from SIF", function () {
     it("should import unweighted workbooks from SIF correctly", function () {
         expect(
@@ -514,4 +521,10 @@ describe("Import from SIF syntactic checker", function () {
         ).to.deep.equal(expectedUnweightedGRNWorkbook);
     });
 
+    it("should throw an error for SIF files with mixed relationship types", function () {
+        expect(
+            importController.sifToGrnsight(sifWithMixedRelationshipTypes).errors[0].errorCode
+        ).to.equal("SIF_MIXED_RELATIONSHIP_TYPE_ERROR");
+    });
+
 });
diff --git a/web-client/public/js/constants.js b/web-client/public/js/constants.js
index f826612a..4f624be5 100644
--- a/web-client/public/js/constants.js
+++ b/web-client/public/js/constants.js
@@ -55,6 +55,7 @@ export const MIN_EDGE_WEIGHT_NORMALIZATION      = 0.0001;
 export const MAX_EDGE_WEIGHT_NORMALIZATION      = 1000;
 
 export const DEFAULT_ZOOM_VALUE                 = 100;
+export const BOUNDARY_MARGIN                    = 5;
 
 export const GREY_EDGE_THRESHOLD_MENU           = "#gray-edge-threshold-menu";
 export const GREY_EDGE_THRESHOLD_SLIDER_SIDEBAR = "#grayThresholdInput";
diff --git a/web-client/public/js/graph.js b/web-client/public/js/graph.js
index c204adbf..cc844469 100644
--- a/web-client/public/js/graph.js
+++ b/web-client/public/js/graph.js
@@ -1,8 +1,13 @@
 import Grid from "d3-v4-grid";
 import { grnState } from "./grnstate";
-import { modifyChargeParameter, modifyLinkDistanceParameter, valueValidator } from "./update-app";
 import {
-    ENDS_IN_EXPRESSION_REGEXP,
+    modifyChargeParameter,
+    modifyLinkDistanceParameter,
+    valueValidator,
+    adjustGeneNameForExpression,
+    hasExpressionData,
+} from "./update-app";
+import {
     VIEWPORT_FIT,
     ZOOM_INPUT,
     ZOOM_PERCENT,
@@ -11,7 +16,8 @@ import {
     ZOOM_DISPLAY_MAXIMUM_VALUE,
     ZOOM_DISPLAY_MIDDLE,
     ZOOM_ADAPTIVE_MAX_SCALE,
-    NETWORK_GRN_MODE
+    NETWORK_GRN_MODE,
+    BOUNDARY_MARGIN
 } from "./constants";
 
 /* globals d3 */
@@ -456,8 +462,6 @@ export var drawGraph = function (workbook) {
             center();
         }
         updateAppBasedOnZoomValue(); // Update zoom value within bounds
-        // Refresh the graph so that nodes and paths are adjusted to fit in viewport
-        tick();
     };
 
     d3.select("#restrict-graph-to-viewport").on("click", function () {
@@ -1087,20 +1091,20 @@ export var drawGraph = function (workbook) {
                 .selectAll(".coloring")
                 .data(function () {
                     if (grnState.workbook.expression[dataset]) {
+                        const geneName = adjustGeneNameForExpression(p);
                         if (
-                            grnState.workbook.expression[dataset].data[p.name]
+                            grnState.workbook.expression[dataset].data[geneName]
                         ) {
                             const result = getExpressionData(
-                                p.name,
+                                geneName,
                                 dataset,
                                 average
                             );
                             timePoints = result.timePoints;
-                            return result.data;
-                        } else {
-                            return 0;
+                            return result.data || [];
                         }
                     }
+                    return [];
                 })
                 .attr("class", "coloring")
                 .enter().append("rect")
@@ -1118,6 +1122,9 @@ export var drawGraph = function (workbook) {
                 .attr("stroke-width", "0px")
                 .style("fill", function (d) {
                     d = d || 0; // missing values are changed to 0
+                    if (d === 0) {
+                        return "white";
+                    }
                     var scale = d3.scaleLinear()
                         .domain([-logFoldChangeMaxValue, logFoldChangeMaxValue])
                         .range([0, 1]);
@@ -1227,15 +1234,6 @@ export var drawGraph = function (workbook) {
         }
     };
 
-    const hasExpressionData = sheets => {
-        for (var property in sheets) {
-            if (property.match(ENDS_IN_EXPRESSION_REGEXP)) {
-                return true;
-            }
-        }
-        return false;
-    };
-
     if (!$.isEmptyObject(workbook.expression) && hasExpressionData(workbook.expression) &&
       grnState.nodeColoring.topDataset !== undefined) {
         updaters.renderNodeColoring();
@@ -1383,8 +1381,6 @@ export var drawGraph = function (workbook) {
         }
     };
 
-    const BOUNDARY_MARGIN = 5;
-
     function viewportBoundsMoveDrag (graphZoom, dx, dy) {
         updateZoomContainerInfo();
         flexibleContainer = calcFlexiBox();
@@ -1526,7 +1522,6 @@ export var drawGraph = function (workbook) {
         try {
             node.attr("x", function (d) {
                 var selfReferringEdge = getSelfReferringEdge(d);
-
                 var selfReferringEdgeWidth = (selfReferringEdge ? getSelfReferringRadius(selfReferringEdge) +
                     selfReferringEdge.strokeWidth + 2 : 0);
                 var rightBoundary = width - (d.textWidth + OFFSET_VALUE) - BOUNDARY_MARGIN - selfReferringEdgeWidth;
@@ -1541,9 +1536,7 @@ export var drawGraph = function (workbook) {
                 }
                 // currentXPos bounds the graph when toggle to !adaptive and moves each of the nodes to be in bounds
                 var currentXPos = Math.max(getLeftXBoundaryMargin(), Math.min(rightBoundary, d.x));
-                if (
-                  adaptive &&
-                  width < MAX_WIDTH &&
+                if (adaptive && width < MAX_WIDTH &&
                   (currentXPos === getLeftXBoundaryMargin() ||
                     currentXPos === rightBoundary)
                 ) {
diff --git a/web-client/public/js/grnstate.js b/web-client/public/js/grnstate.js
index 67b0d011..ffa20b93 100644
--- a/web-client/public/js/grnstate.js
+++ b/web-client/public/js/grnstate.js
@@ -85,6 +85,7 @@ export const grnState = {
         lastDataset: null,
         bottomDataSameAsTop: true,
         nodeColoringOptions: [],
+        ppiNodeColorWarningDisplayed: false,
     },
 
 
diff --git a/web-client/public/js/setup-handlers.js b/web-client/public/js/setup-handlers.js
index c8bec3f7..9c81d86b 100644
--- a/web-client/public/js/setup-handlers.js
+++ b/web-client/public/js/setup-handlers.js
@@ -94,13 +94,11 @@ export const setupHandlers = grnState => {
         window.document.body.appendChild(emptySvg);
         var emptySvgDeclarationComputed = getComputedStyle(emptySvg);
 
-        const traverse = svg => {
-            var tree = [];
-            tree.push(svg);
-            // implement DFS
-            const visit = (node) => {
-                if (node && node.hasChildNodes()) {
-                    var child = node.firstChild;
+        const traverse = (node) => {
+            const tree = [];
+            const visit = (currentNode) => {
+                if (currentNode && currentNode.hasChildNodes()) {
+                    let child = currentNode.firstChild;
                     while (child) {
                         if (child.nodeType === 1 && child.nodeName !== "SCRIPT") {
                             tree.push(child);
@@ -110,38 +108,39 @@ export const setupHandlers = grnState => {
                     }
                 }
             };
-            visit(svg);
+            visit(node);
             return tree;
         };
 
         const explicitlySetStyle = element => {
-            const cSSStyleDeclarationComputed = window.getComputedStyle(element);
-            let i;
-            let len;
-            let key;
-            let value;
-            let computedStyleStr = "";
-
-            for (i = 0, len = cSSStyleDeclarationComputed.length; i < len; i++) {
-                key = cSSStyleDeclarationComputed[i];
-                value = cSSStyleDeclarationComputed.getPropertyValue(key);
+            const cssStyleDeclarationComputed = window.getComputedStyle(element);
+            const computedStyleObj = {};
+
+
+            for (let i = 0; i < cssStyleDeclarationComputed.length; i++) {
+                const key = cssStyleDeclarationComputed[i];
+                const value = cssStyleDeclarationComputed.getPropertyValue(key);
                 if (value !== emptySvgDeclarationComputed.getPropertyValue(key)) {
                     // Don't set computed style of width and height. Makes SVG elmements disappear.
                     if ((key !== "height") && (key !== "width")) {
-                        computedStyleStr += key + ":" + value + ";";
+                        computedStyleObj[key] = value;
                     }
 
                 }
             }
-            element.setAttribute("style", computedStyleStr);
+
+            if (element.classList.contains("weight")) {
+                computedStyleObj["visibility"] = "hidden";
+            }
+
+            if (computedStyleObj) {
+                Object.assign(element.style, computedStyleObj);
+            }
         };
 
         // hardcode computed css styles inside svg
         var allElements = traverse(svg);
-        var i = allElements.length;
-        while (i--) {
-            explicitlySetStyle(allElements[i]);
-        }
+        allElements.forEach(explicitlySetStyle);
     };
 
     const sourceAttributeSetter = (svg) => {
@@ -160,7 +159,7 @@ export const setupHandlers = grnState => {
     };
 
     const exportSVG = (svgElement, name) => {
-        let source = svgElement;
+        let source = svgElement.cloneNode(true);
 
         sourceAttributeSetter(source);
         setInlineStyles(source);
@@ -185,10 +184,30 @@ export const setupHandlers = grnState => {
         const imgData = canvas.toDataURL("image/png");
 
         const pdf = new jsPDF("l", "mm", "letter");
-        const width = pdf.internal.pageSize.getWidth();
-        const height = pdf.internal.pageSize.getHeight();
+        const pdfWidth = pdf.internal.pageSize.getWidth();
+        const pdfHeight = pdf.internal.pageSize.getHeight();
+
+        const svgWidth = canvas.width;
+        const svgHeight = canvas.height;
+
+        const aspectRatio = svgWidth / svgHeight;
+        let scaledWidth = pdfWidth;
+        // ratio = width/height --> height = width/ratio
+        let scaledHeight = scaledWidth / aspectRatio;
+
+        if (scaledHeight > pdfHeight) {
+            scaledHeight = pdfHeight;
+            scaledWidth = pdfHeight * aspectRatio;
+        }
 
-        pdf.addImage(imgData, "PNG", 0, 0, width, height);
+        pdf.addImage(
+            imgData,
+            "PNG",
+            (pdfWidth - scaledWidth) / 2,
+            (pdfHeight - scaledHeight) / 2,
+            scaledWidth,
+            scaledHeight
+        );
         pdf.save(name);
     };
 
@@ -209,7 +228,7 @@ export const setupHandlers = grnState => {
     $(EXPORT_TO_PNG).click(() => {
         var svgContainer = document.getElementById("exportContainer");
         var editedName = grnState.name.replace(determineFileType(grnState.name), "") + ".png";
-        saveSvgAsPng(svgContainer, editedName);
+        saveSvgAsPng(svgContainer, editedName, { backgroundColor: "white"});
     });
 
     $(EXPORT_TO_SVG).click(() => {
diff --git a/web-client/public/js/setup-load-and-import-handlers.js b/web-client/public/js/setup-load-and-import-handlers.js
index 1e52fd5e..c6f80dbf 100644
--- a/web-client/public/js/setup-load-and-import-handlers.js
+++ b/web-client/public/js/setup-load-and-import-handlers.js
@@ -171,8 +171,8 @@ export const setupLoadAndImportHandlers = (grnState) => {
      * for helping to resolve this.
      */
 
-    // $(".upload").change(uploadHandler(loadGrn));
     $("body").on("change", ".upload", uploadHandler(loadGrn));
+
     const loadDemo = (url, value) => {
         $("#demoSourceDropdown option[value='" + value.substring(1) + "']").prop(
             "selected",
diff --git a/web-client/public/js/update-app.js b/web-client/public/js/update-app.js
index 48797d7a..abb76750 100644
--- a/web-client/public/js/update-app.js
+++ b/web-client/public/js/update-app.js
@@ -1,6 +1,6 @@
 import { drawGraph, updaters } from "./graph";
 import { uploadState } from "./upload";
-import { displayWarnings } from "./warnings";
+import { displayWarnings, displayPPINodeColorWarning } from "./warnings";
 import { max } from "d3-array";
 import { grnState } from "./grnstate";
 
@@ -109,7 +109,7 @@ import {
   NETWORK_MODE_GRN,
   EXPORT_TO_UNWEIGHTED_GML_MENU,
   NETWORK_GRN_MODE,
-  NETWORK_PPI_MODE
+  NETWORK_PPI_MODE,
 //   EXPRESSION_SOURCE,
 } from "./constants";
 
@@ -384,6 +384,14 @@ const enableNodeColoringUI = function () {
     $(LOG_FOLD_CHANGE_MAX_VALUE_HEADER).removeClass("hidden");
 };
 
+const adjustGeneNameForExpression = function (gene) {
+    const geneName = gene.name;
+    return grnState.workbook.meta.data.workbookType === NETWORK_PPI_MODE &&
+        geneName.endsWith("p")
+        ? geneName.slice(0, -1)
+        : geneName;
+};
+
 const loadExpressionDatabase = function (isTopDataset) {
     const dataset = isTopDataset ? grnState.nodeColoring.topDataset : grnState.nodeColoring.bottomDataset;
     startLoadingIcon();
@@ -394,7 +402,9 @@ const loadExpressionDatabase = function (isTopDataset) {
         queryExpressionDatabase({
             type:"ExpressionData",
             dataset,
-            genes : grnState.workbook.genes.map(gene => {return gene.name;}).join(","),
+            genes: grnState.workbook.genes
+                    .map(adjustGeneNameForExpression)
+                    .join(","),
             timepoints: timepointsResponse[dataset]
         }).then(function (response) {
             if (isTopDataset) {
@@ -502,6 +512,10 @@ const toggleLayout = (on, off) => {
     }
 };
 
+export const hasExpressionData = (sheets) => {
+    return Object.keys(sheets).some(property => property.match(ENDS_IN_EXPRESSION_REGEXP));
+};
+
 const updatetoForceGraph = () => {};
 
 const updatetoGridLayout = () => {};
@@ -528,7 +542,6 @@ const isNewWorkbook = (name) => {
 };
 
 // Workbook Mode Functions
-
 const updateModeViews = () =>{
     // Select correct dropdown item
     $(`${NETWORK_MODE_DROPDOWN} option`).removeAttr("selected");
@@ -543,14 +556,18 @@ const updateModeViews = () =>{
 };
 
 const checkWorkbookModeSettings = () => {
-    if (grnState.mode === NETWORK_PPI_MODE) {
+    const hasExpression = hasExpressionData(grnState.workbook.expression);
+
+    if (grnState.mode === NETWORK_PPI_MODE || !hasExpression) {
         grnState.nodeColoring.nodeColoringEnabled = false;
+        grnState.nodeColoring.showMenu = true;
         grnState.colorOptimal = false;
-        disableNodeColoringMenus();
+        showNodeColoringMenus();
         hideEdgeWeightOptions();
         updateModeViews();
     } else if (grnState.mode === NETWORK_GRN_MODE) {
         grnState.nodeColoring.nodeColoringEnabled = true;
+        grnState.nodeColoring.showMenu = true;
         grnState.colorOptimal = true;
         showNodeColoringMenus();
         showEdgeWeightOptions();
@@ -587,15 +604,6 @@ const shortenExpressionSheetName = (name) => {
       (name.slice(0, MAX_NUM_CHARACTERS_DROPDOWN) + "...") : name;
 };
 
-const hasExpressionData = (sheets) => {
-    for (var property in sheets) {
-        if (property.match(ENDS_IN_EXPRESSION_REGEXP)) {
-            return true;
-        }
-    }
-    return false;
-};
-
 const updateSpeciesMenu = () => {
     $(SPECIES_DISPLAY).val(grnState.genePageData.species);
     $(SPECIES_BUTTON_CRESS + " span").removeClass("glyphicon-ok");
@@ -878,6 +886,10 @@ export const updateApp = grnState => {
         $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden");
         $(NODE_COLORING_MENU).removeClass("hidden");
         $(NODE_COLORING_NAVBAR_OPTIONS).removeClass("hidden");
+        if (grnState.mode === NETWORK_PPI_MODE) {
+            displayPPINodeColorWarning(grnState.ppiNodeColorWarningDisplayed);
+            grnState.ppiNodeColorWarningDisplayed = true;
+        }
         if (grnState.database.expressionDatasets.includes(grnState.nodeColoring.topDataset) &&
         grnState.workbook.expression[grnState.nodeColoring.topDataset] === undefined) {
             if ($(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked")) {
@@ -905,6 +917,12 @@ export const updateApp = grnState => {
         grnState.nodeColoring.topDataset : "Dahlquist_2018_wt";
         grnState.nodeColoring.bottomDataset = grnState.nodeColoring.bottomDataset ?
         grnState.nodeColoring.bottomDataset : "Dahlquist_2018_wt";
+        $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", true);
+        $(`${NODE_COLORING_TOGGLE_MENU} span`).addClass("glyphicon-ok");
+        $(NODE_COLORING_SIDEBAR_BODY).removeClass("hidden");
+        $(NODE_COLORING_MENU).removeClass("hidden");
+        $(NODE_COLORING_NAVBAR_OPTIONS).removeClass("hidden");
+        $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).val(DEFAULT_MAX_LOG_FOLD_CHANGE);
         $(LOG_FOLD_CHANGE_MAX_VALUE_CLASS).addClass("hidden");
         $(LOG_FOLD_CHANGE_MAX_VALUE_SIDEBAR_BUTTON).addClass("hidden");
         $(LOG_FOLD_CHANGE_MAX_VALUE_HEADER).addClass("hidden");
@@ -931,7 +949,10 @@ export const updateApp = grnState => {
                 //   Investigate why a timeout is required in order for node coloring to take place
                 //   successfully in this case.
                 setTimeout(() => updaters.renderNodeColoring(), 250);
-
+            }
+            if (grnState.mode === NETWORK_PPI_MODE) {
+                displayPPINodeColorWarning(grnState.ppiNodeColorWarningDisplayed);
+                grnState.ppiNodeColorWarningDisplayed = true;
             }
         }
     } else if (grnState.workbook !== null && !grnState.nodeColoring.nodeColoringEnabled) {
@@ -940,6 +961,9 @@ export const updateApp = grnState => {
         $(NODE_COLORING_NAVBAR_OPTIONS).addClass("hidden");
         $(`${NODE_COLORING_TOGGLE_MENU} span`).removeClass("glyphicon-ok");
         $(NODE_COLORING_TOGGLE_SIDEBAR).prop("checked", false);
+        if (grnState.mode === NETWORK_PPI_MODE) {
+            grnState.ppiNodeColorWarningDisplayed = false;
+        }
     }
 
     if (grnState.workbook !== null &&  grnState.workbook.sheetType === "weighted") {
@@ -1010,4 +1034,4 @@ export const updateApp = grnState => {
 };
 
 
-export { stopLoadingIcon, startLoadingIcon};
\ No newline at end of file
+export { stopLoadingIcon, startLoadingIcon, adjustGeneNameForExpression};
\ No newline at end of file
diff --git a/web-client/public/js/upload.js b/web-client/public/js/upload.js
index 50ac8d39..b5340e3e 100644
--- a/web-client/public/js/upload.js
+++ b/web-client/public/js/upload.js
@@ -120,7 +120,7 @@ export const upload = function () {
     const updateOptimizationParameters = (finalExportSheets) => {
         let optimizationParameters = {
             data: grnState.mode === NETWORK_GRN_MODE ? {
-                alpha: 0.002,
+                alpha: 0.02,
                 "kk_max": 1,
                 MaxIter: 100000000,
                 TolFun: 0.000001,
@@ -261,7 +261,7 @@ export const upload = function () {
             } else if (sheet === "network") {
                 finalExportSheets.networks[sheet] = grnState.workbook.network;
             } else if (sheet === "network_weights") {
-                finalExportSheets.networks[sheet] = grnState.workbook.networkWeights;
+                finalExportSheets.networks[sheet] = grnState.workbook.network; // network_weights is identical to network
             } else if (sheet === "optimization_diagnostics") { // Get the additional Sheets
                 finalExportSheets[sheet] = grnState.workbook.meta2;
             } else if (sheet === "optimization_parameters") {
@@ -430,7 +430,7 @@ export const upload = function () {
         let networks = [
             [grnState.workbook.network !== undefined, "network"],
             [grnState.workbook.networkOptimizedWeights !== undefined, "network_optimized_weights"],
-            [grnState.workbook.networkWeights !== undefined, "network_weights"]];
+            [grnState.workbook.network !== undefined, "network_weights"]]; // network_weights is always available if network is available
         // networks = networks.filter(x => x !== false);
         let additionalsheets = grnState.workbook.twoColumnSheets ? [
             ...Object.keys(grnState.workbook.twoColumnSheets),
diff --git a/web-client/public/js/warnings.js b/web-client/public/js/warnings.js
index f17ad80e..61223d9d 100644
--- a/web-client/public/js/warnings.js
+++ b/web-client/public/js/warnings.js
@@ -58,3 +58,28 @@ export var displayWarnings = function (warnings) {
 
     $("#warningsModal").modal("show");
 };
+
+export var displayPPINodeColorWarning = function (warningDisplayed) {
+    if (warningDisplayed) {
+        return;
+    }
+
+    $("#warningIntro").html("Protein-protein interaction node coloring warning.");
+    $("#warningsList").html(
+      ["You are displaying mRNA-level expression data on a protein-protein interaction network.",
+          "Please note that this may not be the most appropriate representation of the data."].join(" ")
+    );
+
+    var screenHeight = $(window).height();
+    var MIN_SCREEN_HEIGHT = 600;
+    var BORDER = 425;
+    var setPanel = screenHeight - BORDER + "px";
+    var minPanel = MIN_SCREEN_HEIGHT - BORDER + "px";
+    if (screenHeight > MIN_SCREEN_HEIGHT) {
+        $("#list-frame").css({ height: setPanel });
+    } else {
+        $("#list-frame").css({ height: minPanel });
+    }
+
+    $("#warningsModal").modal("show");
+};
diff --git a/web-client/views/upload.pug b/web-client/views/upload.pug
index 7132c0bd..a92dc8a9 100644
--- a/web-client/views/upload.pug
+++ b/web-client/views/upload.pug
@@ -513,7 +513,7 @@ html
             p(id='error')
           div(class='modal-footer')
             input(type='button' class='btn btn-default' data-dismiss='modal' value='Close')
-            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('.upload').click()")
+            input(type='button' id='launchFileOpen' class='btn btn-primary' data-dismiss='modal' value='Select New File' onclick="$('#upload-network').click()")
 
     div(id='warningsModal' class='modal fade' tab-index='-1' role='dialog' aria-labelledby='mySmallModalLabel' aria-hidden='true' data-backdrop="static")
       div(class='modal-dialog')