-
Notifications
You must be signed in to change notification settings - Fork 1
/
teaching.html
374 lines (304 loc) · 10.4 KB
/
teaching.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title></title>
<script src="site_libs/jquery/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap/css/flatly.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap/shim/respond.min.js"></script>
<script src="site_libs/jqueryui/jquery-ui.min.js"></script>
<link href="site_libs/tocify/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify/jquery.tocify.js"></script>
<script src="site_libs/navigation/tabsets.js"></script>
<link href="site_libs/highlightjs/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs/highlight.js"></script>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 60px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 65px;
margin-top: -65px;
}
.section h2 {
padding-top: 65px;
margin-top: -65px;
}
.section h3 {
padding-top: 65px;
margin-top: -65px;
}
.section h4 {
padding-top: 65px;
margin-top: -65px;
}
.section h5 {
padding-top: 65px;
margin-top: -65px;
}
.section h6 {
padding-top: 65px;
margin-top: -65px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<div class="container-fluid main-container">
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<script>
$(document).ready(function () {
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
// establish options
var options = {
selectors: "h1,h2,h3",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = true;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
padding-left: 25px;
text-indent: 0;
}
.tocify .list-group-item {
border-radius: 0px;
}
</style>
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Berndsen Lab Website</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="about.html">About</a>
</li>
<li>
<a href="news.html">News</a>
</li>
<li>
<a href="shiny.html">Shiny Apps for Biochemistry</a>
</li>
<li>
<a href="research.html">Research</a>
</li>
<li>
<a href="teaching.html">Teaching</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
</div>
<p>In classes and instructional laboratories, I am interested in finding ways for students to apply and share their knowledge and enthusiasm for Biochemistry in the “real world”. These activities support the <a href="https://www.jmu.edu/chemistry/">JMU Department of Chemistry and Biochemistry’s</a> mission for students to: “Have broad-based problem-solving and communication skills that foster successful career transitions as the scientific community responds to global changes.” Through projects such as those described below students gain more experience as scientists and greater depth of knowledge in the field.</p>
<div id="course-based-undergraduate-research-experiences" class="section level2">
<h2>Course-based Undergraduate Research Experiences</h2>
<p>In this project, students determine the molecular basis for a phenotype modeling a protein structure containing an uncharacterized mutation. This provides a research-based learning experience for the students and helps them apply their lecture knowledge to a new system. An early description of this project can be found in <a href="http://onlinelibrary.wiley.com/doi/10.1002/bmb.20976/abstract"><em>Biochemistry and Molecular Biology Education</em></a>.</p>
<p>Currently, I am continuing to develop infrastructure and lessons to make this type of activity successful in large lecture classes of >75 students. I am grateful to the <a href="https://osf.io/">Open Science Framework</a> for providing a collaborative space for students to work on this project. <a href="https://ceberndsen.github.io/OSF-CGEMS-present-2018/#1">This presentation</a> from the 2018 CGEMS workshop shows some of the basic ideas of using OSF for lab and lecture management.</p>
<div id="recent-publications-using-data-from-cures" class="section level4">
<h4>Recent publications using data from CUREs</h4>
<p><strong>Hossain, RA, Dunham, NR</strong>, Enke RA, Berndsen CE, In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements, Molecular Vision 2018; 24:218-230 <a href="http://www.molvis.org/molvis/v24/218/">link</a></p>
<p>Berndsen CE, <strong>Young BH</strong>, <strong>McCormick QJ</strong>, Enke RA. Connecting common genetic polymorphisms to protein function: A modular project sequence for lecture or lab. Biochem Mol Biol Educ. 2016 Nov 12;44(6):526-536. doi: <a href="http://onlinelibrary.wiley.com/doi/10.1002/bmb.20976/abstract;jsessionid=E705E1670A6276D4A8CEA66DEC1892F8.f02t04">10.1002/bmb.20976.</a> Epub 2016 Jun 9. PMID: 27277577</p>
</div>
</div>
<div id="shiny-apps" class="section level2">
<h2>Shiny Apps</h2>
<p>Students in Biochemistry use a variety of resources in class including <a href="https://ceberndsen.github.io/shiny.html">web-based apps</a> which simulate biochemical experiments. Students learn how to interpret the basics of these data and how to display data for each technique. This is an ongoing project.</p>
</div>
<div id="proteopedia" class="section level2">
<h2>Proteopedia</h2>
<p>Students in Biochemistry I often create <a href="http://proteopedia.org/wiki/index.php/Main_Page">Proteopedia</a> pages explaining various topics of their choosing related to protein biochemistry and structure. This activity help students apply their knowledge of protein structure and function from class using examples in the literature and gain practice explaining complex science to a general audience.</p>
<p>A full <a href="http://proteopedia.org/wiki/index.php/Christopher_Berndsen/Proteopedia">list</a> of previous student projects can be found here.</p>
</div>
<div id="web-based-resources" class="section level2">
<h2>Web-based resources</h2>
<p>In addition to the above, I have written resources for students on certain topics. This list will expand with time and need.</p>
<p><a href="CEBerndsen.github.io/satcurvefitting.html">Fitting Saturation curves</a></p>
<p><a href="CEBerndsen.github.io/CD.html">Circular Dichroism</a></p>
<p><a href="CEBerndsen.github.io/Data_Fitting.html">Basics of Data fitting and figures</a></p>
</div>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>