{"id":83,"date":"2014-02-07T10:06:14","date_gmt":"2014-02-07T09:06:14","guid":{"rendered":"http:\/\/www.igst.it\/nettab\/2014\/?page_id=83"},"modified":"2019-11-06T18:07:21","modified_gmt":"2019-11-06T17:07:21","slug":"tutorials","status":"publish","type":"page","link":"http:\/\/www.igst.it\/nettab\/2019\/programme\/tutorials\/","title":{"rendered":"Tutorials"},"content":{"rendered":"
<\/a><\/div>\n
\nFinal Tutorial Programme<\/b><\/p>\n

Registration<\/strong>
\nAttendance to tutorials is subject to the limitations listed below.
\nRegistration for one or both tutorials can be done through the workshop registration form.<\/p>\n

Venue<\/strong>
\nTutorials will be held in the Fisciano campus of the University of Salerno.
\nBoth tutorials will be held in room F2, building F2, of the Campus.<\/b><\/p>\n


\nMap of the Campus (click to enlarge\/download)<\/a><\/p>\n


\nMap of the entrance with directions to venues (click to enlarge\/download)<\/a><\/p>\n

See the document with venue maps and directions<\/a> for detailed information on how to reach the location of tutorials.<\/p>\n

\n

List of tutorials<\/strong><\/p>\n

Tutorial 1, Thursday November 14, 09:00 – 16:00
\nAnalysis of scRNA-seq using R<\/a><\/strong>
\nAnnamaria Carissimo<\/b>, Monika Krzak<\/b>, Dario Righelli<\/b> and Claudia Angelini<\/b>,
\nInstitute for Applied Mathematics “Mauro Picone” (IAC), National Research Council, Naples, Italy.
\nRegistration fee: 10.00 \u20ac<\/p>\n

Tutorial 2, Monday November 11, 09:30 – 17:30
\nLabel-free quantification with OpenMS<\/a><\/strong>
\nOliver Kohlbacher<\/b>, Julianus Pfeuffer<\/b> and Timo Sachsenberg<\/b>,
\nUniversity of Tuebingen, Germany.
\nRegistration fee: 10.00 \u20ac
\n
\nTutorial supported by the German Network for Bioinformatics Infrastructure<\/a>.<\/p>\n

\n

Tutorial 1<\/a>
\nThursday November 14, 09:00 – 16:00
\nAnalysis of scRNA-seq using R<\/b><\/p>\n

Provisional Programme<\/u><\/p>\n\n\n\n\n\n\n\n\n\n
09:00-10:00<\/td>\nIntroduction and brief overview on scRNAseq data analysis<\/td>\n<\/tr>\n
10:00-11:20<\/td>\nSome R packages for creating scRNAseq data object, quality filtering, normalisation, clustering and visualisation: a guided step-by-step example<\/td>\n<\/tr>\n
11:20-11:40<\/td>\nCoffee break<\/td>\n<\/tr>\n
11:40-13:20<\/td>\nGroup analysis: Participants will be divided in 4 groups. Each group has to to perform a specific data analysis on a given dataset<\/td>\n<\/tr>\n
13:20-14:00<\/td>\nLunch break<\/td>\n<\/tr>\n
14:00-15.00<\/td>\nGroup analysis continuation and Group presentation: each group has to make a short 5 minutes presentation of the obtained results<\/td>\n<\/tr>\n
15:00-16:00<\/td>\nDiscussion and an overview of some srRNAseq advanced topics<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Course material will be freely availble as GitHub page<\/p>\n

Requirements: Participants need to bring their laptop with R installed (version 3.5 or above). The following R packages need to be installed:
\nlibrary(scater)
\nlibrary(M3Drop)
\nlibrary(monocle)
\nlibrary(Seurat)
\nlibrary(mclust)
\nlibrary(scran)
\nlibrary(SC3)<\/p>\n

For further information, please refer to Annamaria Carissimo
\n(a.carissimo@na.iac.cnr.it).<\/p>\n

Tutorial speakers<\/h3>\n\n\n\n\n
<\/a><\/td>\n<\/a><\/td>\n<\/a><\/td>\n<\/a><\/td>\n<\/tr>\n
Annamaria Carissimo<\/a>,
\nIAC\/CNR<\/a>, IT<\/td>\n		Monika Krzak<\/a>,
\nIAC\/CNR<\/a>, IT<\/td>\n		Dario Righelli<\/a>,
\nIAC\/CNR<\/a>, IT<\/td>\n		Claudia Angelini<\/a>,
\nIAC\/CNR<\/a>, IT<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
\n

Tutorial 2<\/a><\/b>
\nMonday November 11, 09:30 – 17:30
\nLabel-free quantification with OpenMS<\/strong>
\n
\nTutorial supported by the German Network for Bioinformatics Infrastructure<\/a>.<\/p>\n

Computational mass spectrometry provides important tools and bioinformatic solutions for the analysis of proteomics data. Different methods for label-free quantification have been developed in recent years and were successfully applied in a wide range of studies. Non-targeted methods have shown great potential in unbiased discovery studies.
\nThis de.NBI<\/a> training event introduces key concepts of label-free analysis using workflow-based processing of real-life data sets. We will introduce several open-source software tools for proteomics, primarily focusing on OpenMS<\/a> (http:\/\/www.OpenMS.org\/<\/a>).
\nIn a hands-on session, we will demonstrate how to combine these tools into complex data analysis workflows including visualization of the results. Participants will have the opportunity to bring their own data and design custom analysis workflows together with instructors.
\nFor participants interested in developing their own algorithms and methods within the OpenMS framework, we provide a brief introduction to pyOpenMS \u2013 the python interface to the OpenMS development library.
\nTraining material and handouts will be prepared for both users that want to design proteomic workflows, as well as training material for algorithm and tool developers.
\nThe participants should bring their own laptop computers. Installer versions of required software will be made available. Bringing own data is possible, but not necessary.<\/p>\n

Tutorial speakers<\/h3>\n\n\n\n\n
<\/a><\/td>\n<\/a><\/td>\n<\/a><\/td>\n <\/td>\n<\/tr>\n
Oliver Kohlbacher<\/a>,
\nUniversity of Tuebingen<\/a>, DE<\/td>\n		Julianus Pfeuffer,
\nUniversity of Tuebingen<\/a>, DE<\/td>\n		Timo Sachsenberg,
\nUniversity of Tuebingen<\/a>, DE<\/td>\n		 <\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Julianus Pfeuffer<\/b> is a Ph.D. student in the field of computational mass spectrometry (bottom-up proteomics). He is one of the core developers of OpenMS.
\nTimo Sachsenberg<\/b> is a postdoctoral researcher in the field of computational mass spectrometry. He is one of the core developers of OpenMS.
\nOliver Kohlbacher<\/b> is a professor for applied and translation bioinformatics at University of T\u00fcbingen and the University Hospital T\u00fcbingen as well as a fellow at the Max Planck Institute for Developmental Biology. His groups are currently focusing on research in computational mass spectrometry, structural bioinformatics, translational bioinformatics, and medical informatics.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

Final Tutorial Programme Registration Attendance to tutorials is subject to the limitations listed below. Registration for one or both tutorials can be done through the workshop registration form. Venue Tutorials will be held in the Fisciano campus of the University of Salerno. Both tutorials will be held in room F2, building F2, of the Campus. […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":4001,"menu_order":9,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-83","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/pages\/83","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/comments?post=83"}],"version-history":[{"count":38,"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/pages\/83\/revisions"}],"predecessor-version":[{"id":4518,"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/pages\/83\/revisions\/4518"}],"up":[{"embeddable":true,"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/pages\/4001"}],"wp:attachment":[{"href":"http:\/\/www.igst.it\/nettab\/2019\/wp-json\/wp\/v2\/media?parent=83"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}