6/25/2016 | 1 Agenda for January 24 call: Wiki update (Peter Horvatovich, Netherlands, chr. 5) Submission of data sets from the JPR special issue (Eric Deutsch,PeptideAtlas, US, chr. 0) Peptide ID probability frequency distribution testing method (Ron Beavis, Canada, chr. 17) BGI and RNA-Seq for the chromosome initiative (Siqi Liu, China, chr. 1) Web browsers update (Ping Xu, China, chr. 1 (Caper), Rob Goode, Australia, chr.7 (Proteome Browser), GenomewidePDB, Korea, chr.13, Young-ki Paik) Domain and network analysis (Jin Park, US, chr. 10)

C-HPP (Tiki) Wiki Department of Pharmacy Analytical Biochemistry 6/25/2016 | 2 Peter Horvatovich

Goal: provide a community information exchange platform for C-HPP project, desseminate protocols, SOAPs etc Software: Tiki Wiki 9.2 ( content management system Link: Main concept: main web pages reflected by menu can be mainly edited by admin rigth users. Other registered users can edit main web page of chromosome teams and create arbitrary number of new wiki pages and upload files for attachement. The goal is that chromosome teams edit the main page of their corresponding chromsome listing the most important information under different categories and create new pages to add additional informations. The main chromosome pages is made using a template (see under Chromsome=>Template), which should be present for all teams. Specially headers of templates are important as they are used to extract information from all chromsome teams in Category menu. If headings are modified then information of different categories will be displayed incorrectly making those pages uncomprehesible. The main chromsome peage should contain short information with indication of date for new items added in order to be able to keep track new changes and novel achievements by the C-HPP board. 6/25/2016 | 3 Goal and main concept

6/25/2016 | 4 Home: Main webpage of wiki stating goals and general annoucements. Chromosomes: Main web page of Chromosome teams and temaplates containing categories providing structure for information that should be reported by each teams. If you have suggestion to add modify these categories pls contac admins (currently Meetings: information on different meetings such main C-HPP related congress, Bioinformatics TC etc. If you wishes to add additional meeting category pls contac admins (currently Events: Contains most important events, milestones or news. If you wishes to add additional menu points pls contac admins (currently About: Contains contact us page and web pahe on C-HPP mission. Registered loged-in users see also a submenu on ”Instruction for authors” providing guidelines for authors to edit the web page. Main menu points

6/25/2016 | 5 Group composition: Provide overview of group composition include names, addresses, residing country of PI and participants. Missing Proteins: Providing overview on number of missing proteins. Bioinformatics protocols: information on bioinformatics protocols used or available at the team. Analytical protocols: information on analytical resources and protocoles used by the team. Biological projects: information on team associated biological projects. Data sets: information on data sets made by the team. Special expertise: information on special expertise or resource availabel at team (e.g. Top-down mass spectrometry, specific protocol for particular PTM enrichement and detection. Major achiements: bulletpoints on major achievements. Categories of main Chromosome pages

6/25/2016 | 6 User registration: Users may register by clicking the ”Register” label on login page. User registration administration

6/25/2016 | 7 User registration and rights The following information is needed currently for user registration: These fields should be completed in future with 6 fields asking for: First name, Last name, Institution, City, Coutry, dropdown menu for affiliated chromosome team. After registration, teh administrator(s) of teh page should activate the user acount, which should be confirmed by the user. User is then registered and may edit pages. All user can edit all chromsome main pages, theerfore it is important to make attention to which page you edit. Edit only the Wiki pages of your team!

6/25/2016 | 8 Future developments Include additional 6 fields for user registration. This should be done before the Wiki page is going to production. Make the template text of the main Chromosome pages non-editable by registered users. Administration of C-HPP Tiki CMS Currently the server is administrated by me (Peter Horvatovich, but I would need one or two additional adminsitrator, who can activate user registration request or change main structures and edit main Wiki pages. Volunteers should me. For any information or request concerning the Wiki page send me an !

6/25/2016 | 9 we prominently display next to every HPP-related paper on thehpp.org the location of the datasets, or “No new proteomics data presented” if there are no data that need to be presented. Or “Data submission pending” in bright red letters if there are data that should be made available but have not. Suggestion from Eric Deutsch From Gil Omenn and B/D HPP Notify all authors of JPR January special issue papers who have experimental data that we expect them to upload the datasets and metadata to ProteomeXchange or to PRIDE with instructions to link through ProteomeXchange.

6/25/2016 | 10 links to the chromosome browsers: HPP Chromosome Browsers: The Proteome Browser at Monash University Chromosome-Assembled human Proteome browsER at BPRC GenomewidePDB at Yonsei University Supplied by Eric Deutsch