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10   <title>antiSMASH: Searching for New Antibiotics Using Open Source Tools</title>
11
12   <meta name="description" content="A presentation of the antiSMASH software for Linux.Conf.AU 2012">
13   <meta name="author" content="Kai Blin">
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36 <body>
37
38 <header>
39  <p>antiSMASH: Searching for New Antibiotics Using Open Source Tools</p>
40 </header>
41
42 <article class="deck-container">
43
44 <section class="slide" id="title-slide">
45   <div id="title-slide-logo">
46     <img height="10%" src="antismash_logo.svg">
47   </div>
48   <div id="subtitle">
49     <h4>An Antibiotics and Secondary Metabolites Analysis Shell</h4>
50     Kai Blin<br>
51     Division for Microbiology/Biotechnology
52   </div>
53   </section>
54
55   <section class="slide" id="background">
56   <h1>Biological Background</h2>
57   </section>
58
59   <section class="slide" id="background-biotech">
60   <h1>Biotechnology</h1>
61   </section>
62
63   <section class="slide" id="background-definition">
64     <h2>Biotechnology - Definition</h2>
65
66     <blockquote cite="http://www.cbd.int/convention/articles/?a=cbd-02">
67         [...] any <span id="definition-technological">technological application</span>
68         that uses <span id="definition-biological">biological systems, living organisms,
69         or derivatives thereof</span>, to make or modify
70         <span id="definition-products">products or processes</span> for specific use.
71     </blockquote>
72     <cite>The UN Convention on Biological Diversity</cite>
73     <div class="slide" id="background-definition-technological"></div>
74     <div class="slide" id="background-definition-biological"></div>
75     <div class="slide" id="background-definition-products"></div>
76   </section>
77
78
79
80   <section class="slide" id="cell-animation-begin">
81     <h2>Biotechnology</h2>
82     <div id="cell-canvas"></div>
83     <div class="slide" id="cell-animation-factory"></div>
84   </section>
85
86   <section class="slide" id="background-example-beer">
87     <img src="beer.jpg">
88   </section>
89
90   <section class="slide" id="background-example-insulin">
91     <img src="insulin.jpg">
92   </section>
93
94   <section class="slide" id="bacteria-animation-begin">
95     <h2>Biofactories</h2>
96     <div id="bacteria-canvas"></div>
97     <div class="slide" id="bacteria-animation-grow"></div>
98   </section>
99
100   <section class="slide" id="background-metaphor-machines">
101   <img src="protein_metaphor.svg" height="300">
102   <div class="float-left-small">
103       <div class="slide" id="enzymes"><img src="enzyme.svg"></div>
104       <div class="slide" id="sensors"><img src="protein_sensor.svg"></div>
105       <div class="slide" id="regulators"><img src="protein_regulator.svg"></div>
106       <div class="slide" id="ribosomes"><img src="protein_ribosome.svg"></div>
107   </section>
108
109   <section class="slide" id="background-metaphor-gene-tools">
110     <img src="a_lot_of_proteins.svg">
111   </section>
112
113   <section class="slide" id="background-metaphor-gene-blueprint">
114     <img src="blueprint.svg" height="600">
115     <h3 class="centered">Gene</h3>
116   </section>
117
118   <section class="slide" id="background-protein-vs-enzyme">
119   <h2>Nomenclature</h2>
120   <div class="float-left-large">
121     <div class="slide" id="when-protein"><img src="protein_parts.svg"></div>
122     <div class="slide" id="when-enzyme"><img src="enzyme.svg"></div>
123   </div>
124   </section>
125
126   <section class="slide" id="background-natures-storage-system">
127   <h1>Nature's Storage System</h1>
128   </section>
129
130   <section class="slide" id="background-miescher-lab">
131   <img src="miescherlab.jpg">
132   </section>
133
134   <section class="slide" id="background-dna">
135   <h2>DNA</h2>
136     <div id="dna-canvas"></div>
137     <div class="slide" id="background-dna-single"></div>
138     <div class="slide" id="background-dna-double"></div>
139   </section>
140
141   <section class="slide" id="background-dna-double-helix">
142     <img src="dna_animation_white.gif">
143     <h3 class="centered">DNA double helix</h3>
144   </section>
145
146   <section class="slide" id="background-amino-acids">
147   <h2>Amino Acids</h2>
148     <img src="amino_acids.svg">
149   </section>
150
151   <section class="slide" id="background-codon">
152     <h2>Codon Wheel</h2>
153     <img src="codon_wheel.svg" height="550">
154   </section>
155
156   <section class="slide" id="background-dna-vs-rna">
157     <img src="dna_vs_rna.svg">
158   </section>
159
160   <section class="slide" id="background-central-dogma">
161   <h2>Central Dogma of Molecular Biology</h2>
162   <img src="central_dogma.svg">
163   </section>
164
165   <section class="slide" id="background-gene-cluster">
166   <h2>Gene Cluster</h2>
167   <img src="gene_cluster.svg" width="750">
168   </section>
169
170   <section class="slide" id="background-metabolism">
171   <h1>Metabolism</h1>
172   </section>
173
174   <section class="slide" id="background-metabolism-beer">
175   <h2>Toxic Waste</h2>
176   <img src="beer_recycling.png">
177   </section>
178
179   <section class="slide" id="background-secondary-metabolism">
180   <h2>Secondary Metabolism</h2>
181   <div class="float-left-large">
182     <div class="slide" id="sec-met-pigments"><img src="pigments.jpg"></div>
183     <div class="slide" id="sec-met-antibiotics"><img src="triple_antibiotic.jpg"></div>
184   </div>
185   </section>
186
187   <section class="slide" id="background-streptomycetes">
188   <img src="bio_background.jpg">
189   </section>
190
191   <section class="slide" id="background-antibiotics-classes">
192   <img src="antibiotics_locations_of_action.svg">
193   </section>
194
195   <section class="slide" id="background-antibiotics-fight">
196   <img src="fight.png" height="600">
197   </section>
198
199   <section class="slide" id="background-bioassay">
200   <img src="antibiotics_screening_small.jpg">
201   </section>
202
203   <section class="slide" id="background-fleming">
204   <img src="fleming.jpg">
205   </section>
206
207   <section class="slide" id="background-why-antibiotics">
208   <h2>Why do we need more antibiotics?</h2>
209   <img src="mrsa_map.png" height="550">
210   </section>
211
212   <section class="slide" id="background-antibiotic-resistance">
213   <img src="antibiotic_resistance.svg">
214   </section>
215
216   <section class="slide" id="background-central-dogma-exception">
217   <img src="central_dogma_exception.svg">
218   </section>
219
220   <section class="slide" id="background-nrps">
221   <h2>Non-Ribosomal Peptide Synthesis</h2>
222   <img src="nrps.svg">
223   </section>
224
225   <section class="slide" id="main-talk">
226   <img src="antismash_logo.svg" height="550">
227   </section>
228
229   <section class="slide" id="antismash-languages-used">
230     <h2>Languages Used</h2>
231     <img src="languages_used.png" height="550">
232   </section>
233
234   <section class="slide" id="antismash-schema">
235   <img src="server_architecture_old.png">
236   </section>
237
238   <section class="slide" id="antismash-gene-finding">
239   <h2>Gene Finding</h2>
240   <img src="gene_finding.svg">
241   </section>
242
243   <section class="slide" id="antismash-find-orfs">
244   <h2>ORF Finding Example</h2>
245   <div id="orf-canvas"><img src="sequence_unannotated.svg"></div>
246   <div class="slide" id="antismash-find-orfs-start"></div>
247   <div class="slide" id="antismash-find-orfs-stop"></div>
248   <div class="slide" id="antismash-find-orfs-all"></div>
249   </section>
250
251   <section class="slide" id="antismash-cluster-identification">
252   <h2>Cluster Identification</h2>
253   </section>
254
255   <section class="slide" id="antismash-clusterblast">
256   <h2>Cluster BLAST</h2>
257   </section>
258
259   <section class="slide" id="antismash-smcogs">
260   <h2>Clusters of Orthologous Groups</h2>
261   </section>
262
263   <section class="slide" id="antismash-frontend">
264   <h2>antiSMASH Web Frontend</h2>
265   <ul>
266     <li>Flask</li>
267     <li>Flask-SQLAlchemy</li>
268     <li>MySQL</li>
269     <li>JQuery</li>
270     <li>SVG</li>
271   </ul>
272   </section>
273
274   <section class="slide" id="thanks">
275   <h1>Thank you</h1>
276   </section>
277
278   <section class="slide" id="sources">
279   Pictures used:<br>
280   <a href="pigments.jpg">pigments.jpg</a> by
281   <a href="http://en.wikipedia.org/wiki/File:Indian_pigments.jpg">Dan Brady</a>
282   </section>
283
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302 </article>
303 <footer>
304 <div id="affiliation">Interfakutäres Intstitut für Mikrobiologie und
305 Infektionsmedizin Tübingen (IMIT)
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