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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="protein_reaction.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="protein_reaction.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     <img src="codon_wheel.svg" height="600">
145   </section>
146
147   <section class="slide" id="background-dna-vs-rna">
148     <img src="dna_vs_rna.svg">
149   </section>
150
151   <section class="slide" id="background-central-dogma">
152   <h2>Central Dogma of Molecular Biology</h2>
153   <img src="central_dogma.svg">
154   </section>
155
156   <section class="slide" id="background-gene-cluster">
157   <h2>Gene Cluster</h2>
158   <img src="gene_cluster.svg" width="750">
159   </section>
160
161   <section class="slide" id="background-metabolism">
162   <img src="beer_recycling.png">
163   </section>
164
165   <section class="slide" id="background-secondary-metabolism">
166   <h2>Secondary Metabolism</h2>
167   <div class="float-left-large">
168     <div class="slide" id="sec-met-pigments"><img src="pigments.jpg"></div>
169     <div class="slide" id="sec-met-antibiotics"><img src="triple_antibiotic.jpg"></div>
170   </div>
171   </section>
172
173   <section class="slide" id="background-streptomycetes">
174   <img src="bio_background.jpg">
175   </section>
176
177   <section class="slide" id="background-antibiotics-classes">
178   <img src="antibiotics_locations_of_action.svg">
179   </section>
180
181   <section class="slide" id="background-bioassay">
182   <img src="antibiotics_screening_small.jpg">
183   </section>
184
185   <section class="slide" id="background-fleming">
186   <img src="fleming.jpg">
187   </section>
188
189   <section class="slide" id="background-why-antibiotics">
190   <h2>Why do we need more antibiotics?</h2>
191   <img src="mrsa_map.png" height="550">
192   </section>
193
194   <section class="slide" id="background-antibiotic-resistance">
195   <img src="antibiotic_resistance.svg">
196   </section>
197
198   <section class="slide" id="background-nrps">
199   <h2>Non-Ribosomal Peptide Synthesis</h2>
200   <img src="nrps.svg">
201   </section>
202
203   <section class="slide" id="main-talk">
204   <img src="antismash_logo.svg" height="550">
205   </section>
206
207   <section class="slide" id="antismash-schema">
208   <img src="server_architecture_old.png">
209   </section>
210
211   <section class="slide" id="antismash-gene-finding">
212   <h2>Gene Finding</h2>
213   </section>
214
215   <section class="slide" id="antismash-cluster-identification">
216   <h2>Cluster Identification</h2>
217   </section>
218
219   <section class="slide" id="antismash-clusterblast">
220   <h2>Cluster BLAST</h2>
221   </section>
222
223   <section class="slide" id="antismash-smcogs">
224   <h2>Clusters of Orthologous Groups</h2>
225   </section>
226
227   <section class="slide" id="antismash-frontend">
228   <h2>antiSMASH Web Frontend</h2>
229   <ul>
230     <li>Flask</li>
231     <li>Flask-SQLAlchemy</li>
232     <li>MySQL</li>
233     <li>JQuery</li>
234     <li>SVG</li>
235   </ul>
236   </section>
237
238   <section class="slide" id="thanks">
239   <h1>Thank you</h1>
240   </section>
241
242   <section class="slide" id="sources">
243   Pictures used:<br>
244   <a href="pigments.jpg">pigments.jpg</a> by
245   <a href="http://en.wikipedia.org/wiki/File:Indian_pigments.jpg">Dan Brady</a>
246   </section>
247
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268 <div id="affiliation">Interfakutäres Intstitut für Mikrobiologie und
269 Infektionsmedizin Tübingen (IMIT)
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