annotate partsgenie.xml @ 0:295a21fc55d0 draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 21 Dec 2021 11:21:30 +0000
parents
children ee8403dc0c63
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
1 <tool id="PartsGenie" name="PartsGenie" version="1.0.1">
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
2 <description>An integrated tool for optimizing and sharing synthetic biology parts</description>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
3 <requirements>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
4 <requirement type="package" version="1.0.1">partsgenieclient</requirement>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
5 </requirements>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
7 python -m partsgenie_client
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
8 '$adv.url'
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
9 '$enzymes_file'
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
10 '$taxonomy_id'
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
11 '$parts'
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
12 ]]></command>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
13 <inputs>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
14 <param name="enzymes_file" type="data" format="xml" label="Enzymes" />
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
15 <param name="taxonomy_id" type="integer" value="83333" label="Chassis taxonomy ID" />
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
16 <section name="adv" title="Advanced Options" expanded="false">
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
17 <param name="url" type="text" value="https://partsgenie.micalis.inrae.fr" label="PartsGenie server URL" />
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
18 </section>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
19 </inputs>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
20 <outputs>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
21 <data name="parts" format="xml" label="Parts" />
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
22 </outputs>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
23 <tests>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
24 <test>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
25 <!-- test 1: check if identical outputs are produced with default parameters -->
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
26 <param name="enzymes_file" value="enzymes_lycopene.xml" />
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
27 <output name="parts" file="parts_lycopene_output.xml" ftype="xml" compare="sim_size" />
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
28 </test>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
29 </tests>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
30 <help><![CDATA[
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
31 PartsGenie
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
32 ===========
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
33
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
34 PartsGenie allows for the design and optimisation of novel, reusable synthetic biology parts.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
35
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
36 * **Introduction**\
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
37
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
38 This user interface consists of a number of components:
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
39
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
40 Parts: an interactive drag-and-drop interface for assembling parts from features such as promoters, ribosome binding sites (RBS) and coding sequences (CDS).
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
41 Feature: a panel allowing for the specification of parameters relating to individual features.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
42 Filters: a panel for specifying filters to consider in optimising the parts.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
43 Results: a panel for displaying and querying results of the part optimisations.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
44 In addition, there is also the functionality for saving optimised parts to an instance of JBEI-ICE.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
45
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
46 * **Parts**\
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
47
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
48 The Parts panel offers a simple drag-and-drop interface for defining multiple parts from a collection of features represented as buttons.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
49
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
50 The user can build up a part by dragging-and-dropping features from the palette of grey buttons. Tablet and smartphone users can add features to the part by double-clicking on the feature button in the palette.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
51
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
52 The features available are described below in the feature section.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
53
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
54 Individual parts may be named.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
55
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
56 Upon selecting a given feature, the Feature panel becomes visible, allowing the specification of parameters specific to that feature. Examples of this include an amino acid sequence for a CDS, or a translation initiation rate (TIR) for an RBS. The feature will be bordered by a red warning box until these necessary features are specified.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
57
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
58 Note that a restriction exists such that a RBS must be immediately followed by a CDS. Again, the RBS will be bordered by a red warning box if this restriction is not adhered to.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
59
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
60 In the case of optimising RBS or CDS, an Organism must be specified from the autofill field.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
61
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
62 Multiple parts may be specified, by either clicking the '+' icon, or by duplicating a specified part through the Copy icon. Individual parts can be viewed and edited by clicking the numbered pagination panel. Designs may be deleted, as can individual features within parts.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
63
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
64 Upon completing the set of parts, and adhering to all restrictions, the Submit button will turn green, and the job may be submitted.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
65
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
66 * **Feature**\
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
67
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
68 The Feature panel is viewed on selecting a given feature in the Design panel.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
69 The Feature panel is specific to the selected feature, which can be one of the following types:
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
70
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
71 Defined sequence.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
72 Randomised sequence.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
73 Sequence of defined melting temperature.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
74 Origin of replication.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
75 Promoter.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
76 Ribosome binding site.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
77 Coding sequence.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
78 Fixed coding sequence.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
79 Terminator.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
80
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
81 In each case, an individual Feature can be named.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
82
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
83 In the cases of Defined sequence, Origin of replication, Promoter and Terminator, the only required parameter is the nucleotide Sequence itself. This sequence is fixed and not optimised by the PartsGenie algorithm.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
84
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
85 Randomised sequence requires a Length of the sequence, which is periodically mutated through the optimisation sequence to optimise the part as a whole.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
86
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
87 A Sequence of defined melting temperature requires a defined melting temperature (Tm).
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
88
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
89 Ribosome binding sites require a desired translation initiation rate TIR.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
90
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
91 Coding sequences require an Amino acid sequence to be specified, which may be extracted automatically through the Search Uniprot facility:
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
92
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
93 * **Filters**\
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
94
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
95 The Filters facility allow for the specification of constraints that must be applied during the optimisation process. A Max repeating nucleotides may be specified, preventing long runs of repeating nucleotides which impede synthesis of designed parts. Excluded codons and Excluded restriction sites may be specified.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
96 In all cases, such Filters should be kept to a minimum, as specifying too many unnecessary constraints will increase optimisation time and, in some cases, prevent optimisation altogether. For example, specifying either too few max repeating nucleotides, or too many excluded codons or restriction sites may result in the design space being constraint to such an extent that no valid reverse translation of an amino acid coding sequence exists.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
97
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
98 * **Results**\
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
99
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
100 Upon completion of an optimisation job (including one or more parts), the Results panel is displayed.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
101 The Results panel allows for the inspection of all optimised parts, allowing for the part as a whole, and individual features, to be viewed.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
102
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
103 Individual features can be viewed by selecting the feature, and metadata specific to that feature can be inspected. (This may include TIR for a RBS, or Codon Adaptation Index (CAI) - a measure of how optimised codon usage is for the target host organism - for CDS features.)
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
104
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
105 * **ICE**\
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
106
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
107 Upon clicking the ICE button, the user is presented with a form for logging into an instance of JBEI ICE. The required parameters are URL of the JBEI ICE instance, Username and Password. Finally, a Group may be specified, allowing any submitted designed part to be shared between members of a JBEI ICE defined group.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
108 Once a user has logged into ICE, the ICE button will turn green, after which, parts may be Saved to JBEI ICE from the Results panel.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
109
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
110 Input
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
111 -----
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
112
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
113 * **infile**\ : (string) Specify input (SBOL) file.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
114 * **taxonomy_id**\ : (integer) The NCBI taxonomy id of the target host organism (Default=83333).
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
115 * **url**\ : (string) The URL of the PartsGenie server.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
116
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
117
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
118 Output
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
119 ------
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
120
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
121 * **outfile**\ : (string) Filename to store the modified SBOL input file.
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
122
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
123
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
124 Project Links
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
125 ---------------------
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
126
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
127 * `GitHub <https://github.com/neilswainston/PartsGenieClient/>`_
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
128
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
129
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
130 Version
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
131 ----------
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
132
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
133 1.0.1
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
134
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
135 Authors
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
136 -------
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
137
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
138 * **Neil Swainston**
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
139 * **Joan Hérisson**
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
140
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
141 License
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
142 -------
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
143
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
144 `MIT <https://github.com/neilswainston/PartsGenieClient/blob/master/LICENSE>`_
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
145 ]]></help>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
146 <citations>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
147 <citation type="bibtex">
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
148 @article{8dc3e3be28b540bc928664e9ff6204e3,
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
149 title = "PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
150 abstract = "Synthetic biology is typified by developing novel genetic constructs from the assembly of reusable synthetic DNA parts, which contain one or more features such as promoters, ribosome binding sites, coding sequences and terminators. PartsGenie is introduced to facilitate the computational design of such synthetic biology parts, bridging the gap between optimization tools for the design of novel parts, the representation of such parts in community-developed data standards such as Synthetic Biology Open Language, and their sharing in journal-recommended data repositories. Consisting of a drag-and-drop web interface, a number of DNA optimization algorithms, and an interface to the well-used data repository JBEI ICE, PartsGenie facilitates the design, optimization and dissemination of reusable synthetic biology parts through an integrated application.",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
151 author = "Neil Swainston and Mark Dunstan and Jervis, {Adrian J} and Robinson, {Christopher J} and Pablo Carbonell and Williams, {Alan R} and Jean-loup Faulon and Scrutton, {Nigel S} and Kell, {Douglas B}",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
152 year = "2018",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
153 month = jul,
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
154 day = "1",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
155 doi = "10.1093/bioinformatics/bty105",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
156 language = "English",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
157 volume = "34",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
158 journal = "Bioinformatics (Oxford, England)",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
159 issn = "1367-4803",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
160 publisher = "Oxford University Press",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
161 number = "12",
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
162 }
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
163 </citation>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
164 </citations>
295a21fc55d0 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
tduigou
parents:
diff changeset
165 </tool>