presentation

presentations/20230915/actors.js

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+import * as regression from 'https://cdn.skypack.dev/d3-regression';
+import * as d3 from 'https://cdn.skypack.dev/d3';
+
+export function plotActors(actors, talentWeight, looksWeight, minimum) {
+
+  actors = transpose(actors).map(v => ({
+    talent: v.x,
+    looks: v.y,
+    fame: v.x * talentWeight + v.y * looksWeight
+  }));
+
+  const w = 600;
+  const h = 470;
+  const result = d3.create("svg").attr("width", w).attr("height", h);
+  const margin = 20;
+  const xScale = d3.scaleLinear().domain([-2, 2]).range([margin, w - margin]);
+  const yScale = d3.scaleLinear().domain([-2, 2]).range([h - margin, margin]);
+  const points = result
+    .append("g")
+    .selectAll("circle")
+    .data(actors)
+    .join(enter => {
+       const sel = enter
+         .append("circle")
+         .attr("r", 3)
+         .attr("cx", d => xScale(d.talent))
+         .attr("cy", d => yScale(d.looks))
+         .attr("fill", d3.lab(50, 40, 20));
+       return sel.filter(d => d.fame <= minimum)
+         .attr("fill", "rgb(200, 200, 200)")
+         .attr("r", 2);
+    });
+
+  const linearRegression = regression.regressionLinear()
+    .x(d => d.talent)
+    .y(d => d.looks)
+    .domain([-2, 2]);
+
+  const chosenActors = actors
+    .filter(d => d.fame > minimum);
+
+  const line = result
+    .append("g")
+    .append("line")
+    .attr("stroke", d3.lab(20, 40, 20))
+    .attr("stroke-width", 1.5)
+    .datum(linearRegression(chosenActors))
+    .attr("x1", d => xScale(d[0][0]))
+    .attr("x2", d => xScale(d[1][0]))
+    .attr("y1", d => yScale(d[0][1]))
+    .attr("y2", d => yScale(d[1][1]));
+
+
+  const xAxis = d3.axisBottom(xScale).ticks(3);
+  result.append("g")
+    .attr("transform", `translate(0, ${yScale(0)})`)
+    .call(xAxis);
+
+  result.append("text")
+    .attr("x", xScale(0.05))
+    .attr("y", yScale(2))
+    .text("Looks");
+
+  result.append("text")
+    .attr("y", yScale(0.1))
+    .attr("x", xScale(-2))
+    .text("Talent");
+
+  const yAxis = d3.axisLeft(yScale).ticks(3);
+  result.append("g")
+    .attr("transform", `translate(${xScale(0)}, 0)`)
+    .call(yAxis);
+
+  return result.node();
+}
+
+function transpose(df) {
+  const keys = Object.keys(df);
+  return df[keys[0]]
+    .map((v, i) => Object.fromEntries(keys.map(key => [key, df[key][i] || undefined])))
+    .filter(v => Object.values(v).every(e => e !== undefined));
+}
+
+
+

presentations/20230915/index.qmd

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+---
+title: "Progress"
+subtitle: "**Daniel Fürth**<br> Assistant professor<br> SciLifeLab/Uppsala University<br><br>🔗 [furthlab.xyz](https://furthlab.xyz)<br>[{{< fa brands twitter size=1xl >}} @furthlab](https://furthlab.xyz)"
+format:
+  revealjs: 
+    slide-number: true
+    chalkboard: 
+      buttons: false
+    preview-links: auto
+    logo: ../assets/img/SciLifeLab_Logotype_Green_POS.png
+    css: styles.css
+    footer: Friday 15 Sep
+    height: 1048
+    width: 1600
+resources:
+  - demo.pdf
+---
+
+## <span style="font-size: 0.7em;">📚🙇🏽‍♀️🙇🏻‍♂️📖 Agenda </span>
+
+<style>
+  .sm {
+  font-size: 0.75em;
+  }
+    .sm2 {
+  font-size: 0.5em;
+  }
+</style>
+
+::: {.sm}
+::: incremental
+Topics for today:
+
+- **🧬 FluoroProx probes**:
+  - Status figures.
+    - Figure 01
+    - Supplementary Figure 1
+    - Figure 2?
+    - Supplementary Figure 2
+-  **🧬 Photolitography:**
+    - New synthesis route
+    - Janelia Dyes?
+    - 2photon microscope  
+:::
+:::
+
+::: footer
+:::
+
+# FluoroProx probes - _fig. 1_
+<img src="../assets/img/fig01_cMycMax.jpg">
+
+# FluoroProx probes - _Supp.fig. 1_
+<img src="../assets/img/fig_S01_synthesis.png">
+
+# FluoroProx probes - _Fig. 2_ ?
+<img src="../assets/img/EMSA.png">
+
+- [Recombinant human c-Myc protein (Active) (ab169901)](https://www.abcam.com/products/proteins-peptides/recombinant-human-c-myc-protein-active-ab169901.html)
+- [Recombinant Human MAX protein (ab95309)](https://www.abcam.com/products/proteins-peptides/recombinant-human-max-protein-ab95309.html)
+
+Oligonucleotide:
+`GATCAGTTGACCACGTGGTCTGGG`
+
+Suggestion: `/56-FAM/GATCAGTTGACCACGTGGTCTGGG/3AmMO/`
+
+- [5' 6-FAM (Fluorescein) `/56-FAM/`](https://eu.idtdna.com/site/catalog/modifications/product/1108)
+- [3' Amino Modifier `/3AmMO/`](https://eu.idtdna.com/site/catalog/modifications/product/3299)
+
+# Cleavable biotin linkers
+
+[PC-Biotin-PEG4-NHS carbonate](https://broadpharm.com/product/bp-23108)
+
+<img src="https://broadpharm.com/web/images/mol_images/BP-23108.gif" width=50%>
+
+[Disulfide Biotin Alkyne](https://broadpharm.com/product/bp-40312)
+
+<img src="https://broadpharm.com/web/images/mol_images/BP-40312.gif" width=80%>
+
+# FluoroProx probes - _Supp.Fig. 2_
+
+# New synthesis route
+
+<img src="../assets/img/new_synthesis.png">