<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:"\@SimSun";
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
h1
{mso-style-priority:9;
mso-style-link:"Heading 1 Char";
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:24.0pt;
font-family:"Times New Roman","serif";
color:black;
font-weight:bold;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman","serif";
color:black;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
span.Heading1Char
{mso-style-name:"Heading 1 Char";
mso-style-priority:9;
mso-style-link:"Heading 1";
font-family:"Cambria","serif";
color:#365F91;
font-weight:bold;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:"Consolas","serif";
color:black;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:905382228;
mso-list-template-ids:409910458;}
@list l0:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:"Courier New";
mso-bidi-font-family:"Times New Roman";}
@list l1
{mso-list-id:1808545161;
mso-list-template-ids:-201693468;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=NL-BE link=blue vlink=purple><div class=WordSection1><h1>MG-RAST workshop (17-18 Sept 2014)<o:p></o:p></h1><div><p class=MsoNormal>MG-RAST (the Metagenomics RAST; <a href="http://www.google.com/url?q=http%3A%2F%2Fmetagenomics.anl.gov&sa=D&sntz=1&usg=AFQjCNFszZKg0mKLWZXaecm3_13bJKUtsQ">http://metagenomics.anl.gov</a>) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.<o:p></o:p></p></div><p>This 2-day workshop will offer researchers opportunities to analyze shotgun metagenomics high-throughput sequencing datasets with MG-RAST, understand the user interface, provide metadata and perform analysis. Special attention will be paid to the API and the R interface, together with general tips and trick for data processing. Sample data will be provided for hands-on analysis.<o:p></o:p></p><p>This workshop will acquaint researchers with MG-RAST sequence analysis tools, enable them to implement their research with MG-RAST, provide hands-on training with real sequence data and offer opportunities to discuss analysis strategies directly with the MG-RAST developers.<o:p></o:p></p><p><b>Instructors</b><o:p></o:p></p><p>Folker Meyer (Argonne National Laboratory and University of Chicago)<br>Andreas Wilke (Argonne National Laboratory and University of Chicago)<o:p></o:p></p><p><b>Schedule</b><o:p></o:p></p><p>day1: Wednesday September 17, 2014, 9:00-17:30<o:p></o:p></p><ol start=1 type=1><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'>MG-RAST overview and user interface<o:p></o:p></li><ul type=circle><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>browse and search public data<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>understanding the pipeline and its limitations<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>understanding the overview page (a first glance at your data)<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>check primer/probe coverage in Probe Match<o:p></o:p></li></ul><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'>Analysis and comparison with the web interface<o:p></o:p></li><ul type=circle><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>review concepts (abundance profile)<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>adjusting parameters<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>comparison of multiple samples<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level2 lfo1'>exporting data<o:p></o:p></li></ul></ol><p>day2: Thursday September 18, 2014, 9:00-17:30<o:p></o:p></p><ol start=1 type=1><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2'>R Interface (matR) and the API<o:p></o:p></li><ol start=1 type=1><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>using R<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>the MG-RAST API<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>simple script examples using the API<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>exporting from MG-RAST to other software<o:p></o:p></li></ol><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2'>Metadata GSC --- Standards and Data Submission<o:p></o:p></li><ol start=1 type=1><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>GSC genome standards<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>Entering metadata with MetaZen<o:p></o:p></li></ol><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo2'>Specialist topics<o:p></o:p></li><ol start=1 type=1><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>sequence pathology --- common problems with NGS and how to find them<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>to assemble or not to assemble?<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>details on the pipeline<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level2 lfo2'>scripting with MG-RAST<o:p></o:p></li></ol></ol><p><b>Venue</b><o:p></o:p></p><p>The course will be organised in the multimedia room of the Information and Communication Technology Department (DICT) at Ghent University, as this facilty has laptop computers for participants that cannot bring their own. Participants that work on their own laptop computer are invited to install a recent version of Firefox. This venue will be made freely available by DICT, with coffee and soda drinks free of charge for all participants.<o:p></o:p></p><p><b>Organizing committee</b><o:p></o:p></p><p>Prof. Dr. Peter Dawyndt (Ghent University)<br>Prof. Dr. Anne Willems (Ghent University)<br>ir. Bart Mesuere (Ghent University)<br>ir. Caroline De Tender (Institute for Agricultural and Fisheries Research; ILVO)<o:p></o:p></p><p><b>Contact</b><o:p></o:p></p><p>Prof. Dr. Peter Dawyndt<br>Department of Applied Mathematics, Computer Science and Statistics<br>Ghent University<br>phone: +32 9 264 4779<br>email: <a href="mailto:Peter.Dawyndt@UGent.be">Peter.Dawyndt@UGent.be</a><o:p></o:p></p><p>Please fill up <a href="https://docs.google.com/forms/d/1_4awjkASXBa52s1ckdfEv4pcZMIO9MraHerFIlpxEr4/viewform">this form</a> to register your participation to this workshop.<o:p></o:p></p><pre>-- <o:p></o:p></pre><pre>-------------------------------------------------------------------------<o:p></o:p></pre><pre>Prof. Dr. Peter Dawyndt<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Ghent University<o:p></o:p></pre><pre>Department of Applied Mathematics, Computer Science and Statistics (WE02)<o:p></o:p></pre><pre>Krijgslaan 281 (S9)<o:p></o:p></pre><pre>B-9000 Ghent<o:p></o:p></pre><pre>Belgium<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Tel: (32)9.264.47.79<o:p></o:p></pre><pre>Fax: (32)9.264.49.95<o:p></o:p></pre><pre>Email: <a href="mailto:Peter.Dawyndt@UGent.be">Peter.Dawyndt@UGent.be</a><o:p></o:p></pre><pre>-------------------------------------------------------------------------<o:p></o:p></pre></div></body></html>