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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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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-definition">
60     <h2>Biotechnology - Definition</h2>
61
62     <blockquote cite="http://www.cbd.int/convention/articles/?a=cbd-02">
63         [...] any <span id="definition-technological">technological application</span>
64         that uses <span id="definition-biological">biological systems, living organisms,
65         or derivatives thereof</span>, to make or modify
66         <span id="definition-products">products or processes</span> for specific use.
67     </blockquote>
68     <cite>The UN Convention on Biological Diversity</cite>
69     <div class="slide" id="background-definition-technological"></div>
70     <div class="slide" id="background-definition-biological"></div>
71     <div class="slide" id="background-definition-products"></div>
72   </section>
73
74
75
76   <section class="slide" id="cell-animation-begin">
77     <h2>Cell</h2>
78     <div id="cell-canvas"></div>
79     <div class="slide" id="cell-animation-factory"></div>
80   </section>
81
82   <section class="slide" id="background-example-beer">
83     <img src="beer.jpg">
84   </section>
85
86   <section class="slide" id="background-example-insulin">
87     <img src="insulin.jpg">
88   </section>
89
90   <section class="slide" id="bacteria-animation-begin">
91     <h2>Biofactories</h2>
92     <div id="bacteria-canvas"></div>
93     <div class="slide" id="bacteria-animation-grow"></div>
94   </section>
95
96   <section class="slide" id="background-metaphor-machines">
97   <img src="protein_metaphor.svg" height="300">
98   <div class="float-left-small">
99       <div class="slide" id="enzymes"><img src="enzyme.svg"></div>
100       <div class="slide" id="sensors"><img src="protein_sensor.svg"></div>
101       <div class="slide" id="regulators"><img src="protein_regulator.svg"></div>
102       <div class="slide" id="ribosomes"><img src="protein_ribosome.svg"></div>
103   </section>
104
105   <section class="slide" id="background-metaphor-gene-tools">
106     <img src="a_lot_of_proteins.svg">
107   </section>
108
109   <section class="slide" id="background-metaphor-gene-blueprint">
110     <img src="blueprint.svg" height="600">
111     <h3 class="centered">Gene</h3>
112   </section>
113
114   <section class="slide" id="background-protein-vs-enzyme">
115   <h2>Nomenclature</h2>
116   <div class="float-left-large">
117     <div class="slide" id="when-protein"><img src="protein_parts.svg"></div>
118     <div class="slide" id="when-enzyme"><img src="enzyme.svg"></div>
119   </div>
120   </section>
121
122   <section class="slide" id="background-miescher-lab">
123   <img src="miescherlab.jpg">
124   </section>
125
126   <section class="slide" id="background-dna">
127   <h2>DNA</h2>
128     <div id="dna-canvas"></div>
129     <div class="slide" id="background-dna-single"></div>
130     <div class="slide" id="background-dna-double"></div>
131   </section>
132
133   <section class="slide" id="background-dna-double-helix">
134     <img src="dna_animation_white.gif">
135     <h3 class="centered">DNA double helix</h3>
136     </section>
137
138   <section class="slide" id="background-amino-acids">
139   <h2>Amino Acids</h2>
140     <img src="amino_acids.svg">
141   </section>
142
143   <section class="slide" id="background-codon">
144     <h2>Codon Wheel</h2>
145     <img src="codon_wheel.svg" height="550">
146   </section>
147
148   <section class="slide" id="background-dna-vs-rna">
149     <img src="dna_vs_rna.svg">
150   </section>
151
152   <section class="slide" id="background-central-dogma">
153   <h2>Central Dogma of Molecular Biology</h2>
154   <img src="central_dogma.svg">
155   </section>
156
157   <section class="slide" id="background-gene-cluster">
158   <h2>Gene Cluster</h2>
159   <img src="gene_cluster.svg" width="750">
160   </section>
161
162   <section class="slide" id="background-metabolism">
163   <h1>Metabolism</h1>
164   </section>
165
166   <section class="slide" id="background-metabolism-beer">
167   <h2>Toxic Waste</h2>
168   <img src="beer_recycling.png">
169   </section>
170
171   <section class="slide" id="background-secondary-metabolism">
172   <h2>Secondary Metabolism</h2>
173   <div class="float-left-large">
174     <div class="slide" id="sec-met-pigments"><img src="pigments.jpg"></div>
175     <div class="slide" id="sec-met-antibiotics"><img src="triple_antibiotic.jpg"></div>
176   </div>
177   </section>
178
179   <section class="slide" id="background-streptomycetes">
180   <img src="bio_background.jpg">
181   </section>
182
183   <section class="slide" id="background-antibiotics-classes">
184   <img src="antibiotics_locations_of_action.svg">
185   </section>
186
187   <section class="slide" id="background-bioassay">
188   <img src="antibiotics_screening_small.jpg">
189   </section>
190
191   <section class="slide" id="background-fleming">
192   <img src="fleming.jpg">
193   </section>
194
195   <section class="slide" id="background-why-antibiotics">
196   <h2>Why do we need more antibiotics?</h2>
197   <img src="mrsa_map.png" height="550">
198   </section>
199
200   <section class="slide" id="background-antibiotic-resistance">
201   <img src="antibiotic_resistance.svg">
202   </section>
203
204   <section class="slide" id="background-nrps">
205   <h2>Non-Ribosomal Peptide Synthesis</h2>
206   <img src="nrps.svg">
207   </section>
208
209   <section class="slide" id="main-talk">
210   <img src="antismash_logo.svg" height="550">
211   </section>
212
213   <section class="slide" id="antismash-schema">
214   <img src="server_architecture_old.png">
215   </section>
216
217   <section class="slide" id="antismash-gene-finding">
218   <h2>Gene Finding</h2>
219   </section>
220
221   <section class="slide" id="antismash-cluster-identification">
222   <h2>Cluster Identification</h2>
223   </section>
224
225   <section class="slide" id="antismash-clusterblast">
226   <h2>Cluster BLAST</h2>
227   </section>
228
229   <section class="slide" id="antismash-smcogs">
230   <h2>Clusters of Orthologous Groups</h2>
231   </section>
232
233   <section class="slide" id="antismash-frontend">
234   <h2>antiSMASH Web Frontend</h2>
235   <ul>
236     <li>Flask</li>
237     <li>Flask-SQLAlchemy</li>
238     <li>MySQL</li>
239     <li>JQuery</li>
240     <li>SVG</li>
241   </ul>
242   </section>
243
244   <section class="slide" id="thanks">
245   <h1>Thank you</h1>
246   </section>
247
248   <section class="slide" id="sources">
249   Pictures used:<br>
250   <a href="pigments.jpg">pigments.jpg</a> by
251   <a href="http://en.wikipedia.org/wiki/File:Indian_pigments.jpg">Dan Brady</a>
252   </section>
253
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274 <div id="affiliation">Interfakutäres Intstitut für Mikrobiologie und
275 Infektionsmedizin Tübingen (IMIT)
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