typo fixes

razor.py

@@ -11,7 +11,7 @@
 
 # Threshold for Max MCC
 # For detecting signal peptides
-SP_THRESHOLD = 0.62
+SP_THRESHOLD = 0.56
 # For signal peptides from fungi
 FUNGI_THRESHOLD = 0.23
 # For signal peptides with toxic protein

src/components/Documentation/RazorDocumentation.jsx

@@ -17,6 +17,9 @@ import RazorLine from "../Chart/RazorLine";
 import SignalData from "./SignalPeptide_Data.csv.gz";
 import ToxinData from "./Toxin_Data.csv.gz";
 import FungiData from "./Fungi_Data.csv.gz";
+import SignalBenchmark from "./benchmark_sp_new.csv.gz";
+import ToxinBenchmark from "./benchmark_toxins.csv.gz";
+import FungiBenchmark from "./benchmark_fungi.csv.gz";
 
 const data = demoRazor();
 const prot = defaultProteinRazor();
@@ -238,11 +241,11 @@ const RazorDocumentation = (props) => {
                           color="textPrimary"
                         >
                           The number of models with prediction probability
-                          greater than a threshold of 0.62. In this example, a
+                          greater than a threshold of 0.56. In this example, a
                           total of 5 stars indicates that all 5 models predict
                           the input sequence harbours a signal peptide. This
                           threshold shows the highest Matthew's correlation
-                          coefficient on the benchmarking set.
+                          coefficient on the training set.
                         </Typography>
                       }
                     />
@@ -269,8 +272,8 @@ const RazorDocumentation = (props) => {
                           Similar to above, there are 5 distinct models for
                           prediction of each of these classes of signal
                           peptides. The threshold for fungi and toxin are 0.23
-                          and 0.33 respectively. In this example, only 1 model
-                          predicts that the signal peptide may be harboured by a
+                          and 0.33 respectively. In this example, 4 models
+                          predict that the signal peptide may be harboured by a
                           toxin, whereas 3 models predict that the signal
                           peptide is harboured by a fungal protein. If none of
                           these models make a positive prediction, these fields
@@ -384,25 +387,38 @@ const RazorDocumentation = (props) => {
                   <a href={SignalData} download>
                     here
                   </a>
+                  . We also curated a new benchmark set for SP prediction. This
+                  can be downloaded{" "}
+                  <a href={SignalBenchmark} download>
+                    here
+                  </a>
                   .
                 </Typography>
 
                 <Typography variant="body2" gutterBottom>
-                  The dataset used for the toxin signal peptide prediction can
-                  be downloaded{" "}
-                  <a href={FungiData} download>
+                  The dataset used for the toxin signal peptide training and
+                  benchmarking can be downloaded{" "}
+                  <a href={ToxinData} download>
                     here
-                  </a>
-                  .
+                  </a>{" "}
+                  and{" "}
+                  <a href={ToxinBenchmark} download>
+                    here
+                  </a>{" "}
+                  respectively.
                 </Typography>
 
                 <Typography variant="body2" gutterBottom>
-                  The dataset used for the fungal signal peptide prediction can
-                  be downloaded{" "}
-                  <a href={ToxinData} download>
+                  The dataset used for the fungal signal peptide training and
+                  benchmarking can be downloaded{" "}
+                  <a href={FungiData} download>
                     here
-                  </a>
-                  .
+                  </a>{" "}
+                  and{" "}
+                  <a href={FungiBenchmark} download>
+                    here
+                  </a>{" "}
+                  respectively.
                 </Typography>
 
                 <Typography variant="h2" component="h3" gutterBottom>
@@ -469,7 +485,8 @@ const RazorDocumentation = (props) => {
                   Bhandari, B.K., Gardner, P.P., Lim, C.S. (2020) Annotating
                   eukaryotic and toxin-specific signal peptides using Razor.
                   <cite title="Annotating eukaryotic and toxin-specific signal peptides using Razor.">
-                    {" "}bioRxiv.
+                    {" "}
+                    bioRxiv.
                   </cite>{" "}
                   DOI:
                   <a
@@ -488,7 +505,8 @@ const RazorDocumentation = (props) => {
                   Solubility-Weighted Index: fast and accurate prediction of
                   protein solubility.
                   <cite title="Solubility-Weighted Index:  fast and accurate prediction of protein solubility. ">
-                    {" "}Bioinformatics.
+                    {" "}
+                    Bioinformatics.
                   </cite>{" "}
                   DOI:
                   <a

src/components/Documentation/TisignerDocumentation.jsx

@@ -437,7 +437,7 @@ const TisignerDocumentation = (props) => {
                           </a>
                           . If there are any hits, we report the number of those
                           hits and their corresponding E values. If there are no
-                          hits, then these two fields are not displayed.
+                          hits, then this field is not displayed.
                         </Typography>
                       }
                     />
@@ -546,7 +546,9 @@ const TisignerDocumentation = (props) => {
                 </Typography>
                 <Typography variant="body2" gutterBottom>
                   If unsure input the 71 nt vector-encoded sequence preceding
-                  the start codon.
+                  the start codon. For 5&prime; UTRs shorter than 71
+                  nucleotides, upstream sequences can be used to extend the
+                  UTRs.
                 </Typography>
 
                 <Typography variant="subtitle2" gutterBottom>
@@ -630,9 +632,9 @@ const TisignerDocumentation = (props) => {
                   If you find protein solubility prediction and optimisation
                   useful, please cite :
                   <br />
-                  Bhandari, B.K., Gardner, P.P., Lim, C.S.
-                  (2020) Solubility-Weighted Index: Fast and Accurate Prediction
-                  of Protein Solubility.
+                  Bhandari, B.K., Gardner, P.P., Lim, C.S. (2020)
+                  Solubility-Weighted Index: Fast and Accurate Prediction of
+                  Protein Solubility.
                   <cite title="Solubility-Weighted Index: Fast and Accurate Prediction of Protein Solubility ">
                     {" "}
                     Bioinformatics.

src/components/EndPoints.jsx

@@ -1,3 +1,2 @@
-
 export const TIsignerLink = "http://localhost:5050/optimise";
 export const RazorLink = "http://localhost:5050/razor";

src/components/Tisigner/form/Extra.jsx

@@ -205,7 +205,7 @@ class Extra extends Component {
 
         {this.state.substitutionMode === "transInit" ? (
           <div className="control">
-            <label className="label">Maximum number of replacable codons</label>
+            <label className="label">Maximum number of replaceable codons</label>
             <Slider
               value={this.state.numberOfCodons}
               valueLabelDisplay="auto"

src/components/Tisigner/form/General.jsx

@@ -8,31 +8,31 @@ const hosts = [
   { value: "Escherichia coli", label: "Escherichia coli" },
   { value: "Saccharomyces cerevisiae", label: "Saccharomyces cerevisiae" },
   { value: "Mus musculus", label: "Mus musculus" },
-  { value: "Other", label: "Other" }
+  { value: "Other", label: "Other" },
 ];
 
 const promoters = [
   { value: "T7", label: "T7lac promoter (e.g., pET21)" },
-  { value: "Custom", label: "Custom" }
+  { value: "Custom", label: "Custom" },
 ];
 
 const marks = [
   {
     value: 5,
-    label: "5"
+    label: "5",
   },
   {
     value: 30,
-    label: "30 (Low)"
+    label: "30 (Low)",
   },
   {
     value: 70,
-    label: "70 (High)"
+    label: "70 (High)",
   },
   {
     value: 100,
-    label: "100"
-  }
+    label: "100",
+  },
 ];
 
 class General extends Component {
@@ -51,7 +51,7 @@ class General extends Component {
       isValidated:
         JSON.parse(localStorage.getItem("isValidatedGeneral")) !== null
           ? JSON.parse(localStorage.getItem("isValidatedGeneral"))
-          : true
+          : true,
     };
     // this.selectUtr = this.selectUtr.bind(this);
     this._selectHost = this._selectHost.bind(this);
@@ -61,7 +61,7 @@ class General extends Component {
     this.customPromoterInput = this.customPromoterInput.bind(this);
   }
 
-  _selectHost = option => {
+  _selectHost = (option) => {
     // console.log(`You selected ${option.label}, with value ${option.value}`)
     this.setState({
       host: option.value,
@@ -70,50 +70,54 @@ class General extends Component {
         option.value === "Escherichia coli" ? this.state.promoter : "Custom",
       isValidated: false,
       customPromoterError:
-        option.value !== "Escherichia coli" ? "Empty custom promoter." : ""
+        option.value !== "Escherichia coli" ? "Empty custom promoter." : "",
     });
     ReactGA.event({
       category: "TIsigner Customisation",
       action: "Host selected: " + option.value,
-      label: "General"
+      label: "General",
     });
   };
 
-  _selectPromoter = option => {
+  _selectPromoter = (option) => {
     // console.log(`You selected ${option.label}, with value ${option.value}`)
     this.setState({
       promoter: option.value,
       customPromoter: "",
       isValidated: false,
-      customPromoterError: option.value === "T7" ? "" : "Empty custom promoter."
+      customPromoterError:
+        option.value === "T7" ? "" : "Empty custom promoter.",
     });
     ReactGA.event({
       category: "TIsigner Customisation",
       action: "Promoter selected: " + option.value,
-      label: "General"
+      label: "General",
     });
   };
 
   sliderChange = (event, value) => {
     this.setState({
-      targetExpression: value
+      targetExpression: value,
     });
   };
 
   radioChange(event) {
     this.setState({
-      optimisationDirection: event.target.value
+      optimisationDirection: event.target.value,
     });
 
     ReactGA.event({
       category: "TIsigner Customisation",
       action: "Optimisation Direction: " + event.target.value,
-      label: "General"
+      label: "General",
     });
   }
 
   customPromoterInput(event) {
-    let input = event.target.value.replace(/ /g, "").replace(/U/gi, "T").toUpperCase();
+    let input = event.target.value
+      .replace(/ /g, "")
+      .replace(/U/gi, "T")
+      .toUpperCase();
     let promoter = "";
     let filter = /^[ACGTU]+$/;
     let isValid = true;
@@ -135,13 +139,13 @@ class General extends Component {
     this.setState({
       customPromoter: promoter,
       isValidated: this.state.promoter === "T7" ? true : isValid,
-      customPromoterError: errors
+      customPromoterError: errors,
     });
 
     ReactGA.event({
       category: "TIsigner Customisation",
       action: "Custom promoter was entered.",
-      label: "General"
+      label: "General",
     });
   }
 
@@ -152,14 +156,14 @@ class General extends Component {
     !host
       ? localStorage.setItem("host", JSON.stringify(this.state.host))
       : this.setState({
-          host: host
+          host: host,
         });
 
     const promoter = JSON.parse(localStorage.getItem("promoter"));
     !promoter
       ? localStorage.setItem("promoter", JSON.stringify(this.state.promoter))
       : this.setState({
-          promoter: promoter
+          promoter: promoter,
         });
 
     const substitutionMode = JSON.parse(
@@ -171,7 +175,7 @@ class General extends Component {
           JSON.stringify(this.state.substitutionMode)
         )
       : this.setState({
-          substitutionMode: substitutionMode
+          substitutionMode: substitutionMode,
         });
 
     const customPromoter = JSON.parse(localStorage.getItem("customPromoter"));
@@ -181,7 +185,7 @@ class General extends Component {
           JSON.stringify(this.state.customPromoter)
         )
       : this.setState({
-          customPromoter: customPromoter
+          customPromoter: customPromoter,
         });
 
     const targetExpression = JSON.parse(
@@ -193,7 +197,7 @@ class General extends Component {
           JSON.stringify(this.state.targetExpression)
         )
       : this.setState({
-          targetExpression: targetExpression
+          targetExpression: targetExpression,
         });
 
     const optimisationDirection = JSON.parse(
@@ -205,7 +209,7 @@ class General extends Component {
           JSON.stringify(this.state.optimisationDirection)
         )
       : this.setState({
-          optimisationDirection: optimisationDirection
+          optimisationDirection: optimisationDirection,
         });
 
     const isValidated = JSON.parse(localStorage.getItem("isValidatedGeneral"));
@@ -215,7 +219,7 @@ class General extends Component {
           JSON.stringify(this.state.isValidated)
         )
       : this.setState({
-          isValidated: this.state.promoter === "T7" ? true : isValidated
+          isValidated: this.state.promoter === "T7" ? true : isValidated,
         });
 
     const customPromoterError = JSON.parse(
@@ -227,13 +231,13 @@ class General extends Component {
           JSON.stringify(this.state.customPromoterError)
         )
       : this.setState({
-          customPromoterError: !(promoter === "T7") ? customPromoterError : ""
+          customPromoterError: !(promoter === "T7") ? customPromoterError : "",
         });
 
     ReactGA.event({
       category: "TIsigner Customisation",
       action: "General Tab was clicked.",
-      label: "General"
+      label: "General",
     });
   }
 
@@ -312,7 +316,9 @@ class General extends Component {
                   />
                 </div>
                 <p className="help ">
-                  Length should be greater than 70 nucleotides.{" "}
+                  Length should be greater than 70 nucleotides. For 5&prime;
+                  UTRs shorter than 71 nucleotides, upstream sequences can be
+                  used to extend the UTRs.
                 </p>
               </div>
             )}
@@ -367,7 +373,7 @@ class General extends Component {
                 ReactGA.event({
                   category: "TIsigner Customisation",
                   action: "Target Expression: " + this.state.targetExpression,
-                  label: "General"
+                  label: "General",
                 });
               }}
             />