Merge branch 'main' of https://github.com/BranniganLab/blobulator int…

…o production

README.md

@@ -1,10 +1,7 @@
 # Protein Blobulator
-This tool identifies contiguous stretches of hydrophobic residues within a protein sequence. Any sequence of contiguous hydrophobic residues that is at least as long as the minimum blob length is considered an hydrophobic or h "blob". Any remaining segments that are at least as long as the minimum length are considered polar or p "blobs," while those that are shorter than the minimum blob length are considered separator or "s" residues.  Separator residues are very short stretches of non-hydrophobic residues that may be found between two h blobs.
-
-## Web Interface
-
-A web interface for this tool is currently under active development. The alpha version can be found at https://www.blobulator.branniganlab.org/
+_Looking for the webinterface? Try here:_ https://www.blobulator.branniganlab.org/ 
 
+This tool identifies contiguous stretches of hydrophobic residues within a protein sequence. Any sequence of contiguous hydrophobic residues that is at least as long as the minimum blob length is considered an hydrophobic or h "blob". Any remaining segments that are at least as long as the minimum length are considered polar or p "blobs," while those that are shorter than the minimum blob length are considered separator or "s" residues.  Separator residues are very short stretches of non-hydrophobic residues that may be found between two h blobs.
 
 ## Running locally:
 

templates/common-tabcontent.html

@@ -47,7 +47,7 @@ <h4 class="mt-2">Welcome to the Blobulator</h4>
     <p>Blobulation is an approach for edge-detection in protein sequences based on contiguous hydrophobicity, <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007390" target="_blank"> originally developed </a> by the <a href="https://branniganlab.org/" target="_blank"> Brannigan Lab </a> for a specific long intrinsically disordered protein (the prodomain of BDNF). The blobulator allows the user to blobulate any sequence, and visualize the results while adjusting the two blobulation parameters to detect more edges for higher-resolution ("zooming-in") or detect fewer edges for a more tractable visualization ("zooming-out").</p>
     <p> A stretch of residues between two edges are called blobs, inspired by the terminology in polymer physics. The blobulator also characterizes each blob based on several collective properties of the blob residues, including hydrophobicity, net charge, globular tendency (Das-Pappu phase), distance from the Uversky boundary, and sensitivity to mutation. These properties are also dynamically adjusted as the user increases or decreases resolution of the sequence. For human proteins, users will also see the location of disease-associated single nucleotide polymorphisms (SNPs). </p>
     <p>For bug reports, feature requests, or anything else please contact at connor.pitman@rutgers.edu or grace.brannigan@rutgers.edu.</p>
-    <br>Citing the Blobulator<br> <p>A manuscript on the Blobulator is currently in preparation. For now, please cite analysis done with Blobulator using: <a href="https://www.biorxiv.org/content/10.1101/2021.09.02.458776v1" target="_blank"> Lohia R, Hansen M, Brannigan G, “Contiguously hydrophobic sequences are functionally significant throughout the human exome.” BioRxiv. 2021. doi: 10.1101/2021.09.02.458776 </a> </p>
+    <br>Citing the Blobulator<br> <p>A manuscript on the Blobulator is currently in preparation. For now, please cite analysis done with Blobulator using: <a href="https://www.pnas.org/doi/10.1073/pnas.2116267119" target="_blank"> Lohia R, Hansen M, Brannigan G, “Contiguously hydrophobic sequences are functionally significant throughout the human exome.” PNAS. 2022. doi: 10.1073 </a> </p>
 
 </div>
 <!--Documentation Page Contents - styled as accordion panels-->
@@ -99,7 +99,7 @@ <h4 class="mt-2">Interpreting Plots</h4>
     </div>
     <button class="accordion">&#10133 Blobs colored according to dSNP enrichment</button>
     <div class="panel">
-    <p>This fifth outputted visualization shows the blobs according to their enrichment in documented disease associated SNPs (dSNP). This idea was investigated in the context of aggregating and non-aggregating proteins at various blob lengths and hydrophobicity cutoffs in a <a href="https://www.biorxiv.org/content/10.1101/2021.09.02.458776v1" target="blank"> forthcoming paper</a>, from which the figure below is presented (Lohia, et al).</p>
+    <p>This fifth outputted visualization shows the blobs according to their enrichment in documented disease associated SNPs (dSNP). This idea was investigated in the context of aggregating and non-aggregating proteins at various blob lengths and hydrophobicity cutoffs a <a href="https://www.pnas.org/doi/10.1073/pnas.2116267119" target="blank"></a>, from which the figure below is presented (Lohia, et al).</p>
     </div>
     <button class="accordion">&#10133 Blobs colored according to fraction of disordered residue</button>
     <div class="panel">
@@ -120,7 +120,11 @@ <h4 class="mt-2">Frequently Asked Questions:</h4>
 
     <button class="accordion">&#10133 Why do you call them blobs?</button>
     <div class="panel">
-    <p>The nomenclature used here comes from polymer physics, where the segments of a polypeptide chain are grouped together into interaction domains, where the residues within a certain region of the protein can be expected to behave in a relatively predictable way (de Gennes, 1979). Blobs here are determined by defining regions of contihuously hydrophobic residues, and the regions of non-hydrophobic residues that span between. A blob is a contiguous stretch of either hydrophobic or non-hydrophobic residues, and were first classified by the ways that they "stuck" together. </p>
+    <p>The nomenclature used here comes from polymer physics (<a href="https://pubs.acs.org/doi/10.1021/ma60051a002" target="_blank">Pincus, 1976</a>; de Gennes, 1979): a blob is a group of sequential monomers in a polymer chain that "clump" with a characteristic length. For more information see <i>Scaling Concepts in Polymer Physics</i> by Pierre-Gilles de Gennes. </p>
+    </div>
+    <button class="accordion">&#10133 What defines a blob in a protein?</button>
+    <div class="panel">
+    <p>Blobs here are determined by defining regions of contiguously hydrophobic residues, and the regions of non-hydrophobic residues that span between. A blob is a contiguous stretch of either hydrophobic or non-hydrophobic residues greater than a certain length. </p>
     </div>
     <button class="accordion">&#10133 What is the evidence that blobulation is useful?</button>
     <div class="panel">

templates/result.html

@@ -21,7 +21,7 @@
 		"<p> <i> <b> Figure adapted from: </b> <a href=\"https://www.pnas.org/content/early/2013/07/29/1304749110\" target=\"_blank\"> Das RK, Pappu RV (2013) Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues PNAS 110(33):13392–13397.</i> </p>"
 	const ncpr_tool_text = "<p>For each blob its net charge per residue (NCPR) is calculated. Each blob is evaluated based on its fraction of both positively and negatively charged residues. The darker blue a blob is shown here, the higher the fraction of positively charged residues are present within the blob. Alternatively, the darker red a blob is shown here, the higher the fraction of negatively charged residues are present within the blob. An even fraction of positive or negative, or a low fraction of any charged residues, results in a grey color.</p>"
 	const uversky_tool_text = "<p>For each blob its signed normal displacement from the line representing the boundary between ordered (natively folded) and disordered (natively unfolded) proteins on the Uversky diagram (shown below) is plotted. Calculated negative values (represented in orange) are ordered and positive values (shown in blue) are disordered and plotted on the visualization to the left. </p> <img src=\"/static/uversky_plot.png\" width=\"425\" height=\"260\" align=\"center\"> <p> <i> <b> The units on the X and Y axis represent the net charge and hydrophobicity of each blob, normalized on a 0 to 1 scale. Figure adapted from figure 5 in: </b> <a href=\"https://pubmed.ncbi.nlm.nih.gov/11025552/\" target=\"_blank\"> Uversky VN, Gillespie JR, Fink AL (2002) Why are \"natively unfolded\" proteins unstructured under physiologic conditions? </i> </p>"
-	const enrichment_tool_text = "<p>Here, blobs are colored based upon their predicted enrichment in disease associated SNPs (dSNPs), as defined by the results of a previous study. This idea was investigated in the context of proteins at various blob lengths and hydrophobicity cutoffs, the results of which are presented in a <a href=\"https://www.biorxiv.org/content/10.1101/2021.09.02.458776v1\" target=\"blank\"> forthcoming paper</a>, and from which the figure below is presented (Lohia, et al).</p> <img src=\"/static/dsnp_enrich.png\" width=\"450\" height=\"410\">"
+	const enrichment_tool_text = "<p>Here, blobs are colored based upon their predicted enrichment in disease associated SNPs (dSNPs), as defined by the results of a previous study. This idea was investigated in the context of proteins at various blob lengths and hydrophobicity cutoffs, the results of which are presented in <a href=\"https://www.pnas.org/doi/10.1073/pnas.2116267119\" target=\"blank\">this paper</a>, and from which the figure below is presented (Lohia, et al).</p> <img src=\"/static/dsnp_enrich.png\" width=\"450\" height=\"410\">"
 	const disorder_tool_text = "<p>For each blob its fraction of disordered residue is calculated. This disorder calculation is only available if the user uses the Uniprot ID, and uses information provided by the Database of Disordered Protein Prediction. <i> <a href=\"https://academic.oup.com/nar/article/41/D1/D508/1069637\" target=\"_blank\"> Oates et al., D2P2: database of disordered protein predictions, Nucleic Acids Research, Volume 41, Issue D1, 1 January 2013, Pages D508–D516, https://doi.org/10.1093/nar/gks1226</i></p>"
 	const zoom_tool_text = "<p>You can zoom into a region of the protein sequence by clicking and dragging on any of the charts. Zoom out by double-clicking on any chart, or by clicking the Reset Zoom button.</p>"
 
@@ -204,7 +204,6 @@
 				var snp_id = document.getElementById("snp_id").value;
 				var amino_acid = document.getElementById("residue_type").value;
 				my_seq = my_seq.slice(0, snp_id-1) + amino_acid + my_seq.substr(snp_id, my_seq.length);
-				d3.select("").attr("fill", "pink");
 			}
 
 			// Download data