Data files

This Excel template is for use with affy transcriptomics data in Matrix table format. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

Final version of the Agenda: All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock.

Creators: None

Contributor: Olga Krebs

This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.

This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model).
Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.

This template is for recording genome data from the NimbleGen platform.
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

Some home work for PALs to prepare Lightning Talks and ISBE/ESFRI Sessions

Creator: Olga Krebs

Contributor: Olga Krebs

Meeting location map

Creator: Olga Krebs

Contributor: Olga Krebs

This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.

This template is a JERM compliant spreadsheet for use with gel electrophoresis data. It is in the style of the JERM MASTER template with worksheets for metadata, organism_sample, instrument and data. To conform to MIAPE-GE all worksheets are mandatory.
A detailed description of MIAPE-GE is available from http://www.psidev.info/miape/MIAPE_GE_1_4.pdf

This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)

An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.

The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies

An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).

This document outlines our plans for making it easier to publish assets from SEEK to enable people from outside the consortium to see them.

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

An example of a JERM-compliant template for RT-PCR data

This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.

This report gives an overview of the sessions and outcomes from the recent SEEK Users meeting in Berlin.
Please see related 'Presentation' entries for related slides and supplementary material.

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

No description specified

Creator: Franco Du Preez

Contributor: Franco Du Preez

The file contains complete agenda of the SEEK users meeting , 26-27 March 2012 in Berlin

Creator: Olga Krebs

Contributor: Olga Krebs

MIAPE based Gel Electrophoresis Data Entry Worksheet

How to get to the hotel from rail station

Creator: Olga Krebs

Contributor: Olga Krebs

This template is for recording gene expression data from the NimbleGen platform.
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment).
This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

Please fill in thistravel expense reimbursement report and send it together with original receipts to HITS

Creator: Olga Krebs

Contributor: Olga Krebs

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