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e:Med survey


Dear e:Med project members,

On behalf of the e:Med project groups "Informatics and Modelling" and "Epigenetics & Sequencing" we ask you to answer this survey on data and tools you are using in your e:Med project.

The intention of this survey is to get an overview of the tools and data used throughout the projects. Results will be published on the e:Med web page to allow all e:med members to benefit from the expertise available in the program.

The survey will take about ten minutes.

In case of any questions, please feel free to contact me:

Dr. Matthias Ganzinger

Heidelberg University
Institute of Medical Biometry and Informatics
Im Neuenheimer Feld 305
69120 Heidelberg

Phone: +49 6221 56-5143

Email: matthias.ganzinger@med.uni-heidelberg.de

 

Impressum

There are 30 questions in this survey.

General

In this section, we have some general questions on your projects.

 

For which e:Med project are you working?
e:Med research consortium
CancerTelSys
CAPSyS
CLIOMMICS
e:AtheroSysmed
e:Kid
IntegraMent
Multiscale HCC
PANC-STRAT
SMOOSE
SYSIMIT
SysINFLAME
SysMedAlcoholism
SYSMED-NB
SYS-Stomach
e:Med demonstrator
HaematoOPT
HER2Low
MAPTor-NET
Melanoma sensitivity
Mito-PD
MMML-Demonstrators
SMART
SYS-GLIO
e:Med junior research alliance
DeCaRe
GlioPATH
MILES
mitOmics
PsychoSys
SUPR-G
symAtrial
SYMBOL-HF
TIL-REP
Other project
Please specify:
What is your primary role in the project?
Principal investigator
Researcher
PostDoc
Other: 
What is your educational background?
Biology
Medicine
Computer science
Bioinformatics
Medical Informatics
Physics
Biostatistics
Mathematics
Other:
What diseases are covered by your project?

Please specify corresponding ICD codes if you have them at hand:

Please enter your contact details.

Tools

Now we would like to ask you about the IT-tools used in your project.
What IT tools are used in your project?
R with bioconductor (please specify main packages below)
R with other packages (please specify main packages below)
Microsoft Access
Microsoft Excel
Cytoscape
Chenomx NMR Suite
SAS
SPSS
SigmaPlot
Statistica
Own development (please specify below)
Other (please specify below)
Please enter details or comments on your tools here:

Do you have a tool chain or analysis pipeline established?
No
Yes (Please specify)

What tools for data extraction and transformation do you use?
Talend Open Studio
Kettle
KNIME
Other:
What tools for data integration like a data warehouse do you use?
i2b2
tranSMART
SAP HANA
IBM Cognos
Other:

Data

Now we have some questions on the data you are using for your resarch.
What data types are used in your project?
Demographic data
Behavioral data
Environmental data
Physiological data
Examination results
Phenotype data
Laboratory data
Imaging data
Other clinical data
Genomic data
Transcriptomic data
Proteomic data
Metabolomic data
Pathway data
Other (please specify)
Are there any data types you would need for your project that are not available?
Yes
No

What data sources are you using? Please specify.
Electronic medical record
Public database
Literature
Biobank
Data generation for the project
Other (please specify)
Are there data sources you are missing?
No
Yes (Please specify)

Modelling methods

What categories of modelling methods are used in your project? Please detail your specific methods next to the categories.
Regression
Classification
Clustering
Time series
Network analysis
Ordinary differential equation (ODE)
Other (please specify)
What are the endpoints you are studying?
Survival
Disease subtypes
Disease stages
Drug response
Biomarker
Other (please specify)

Biomaterial

In this section, we would like to know, if you are using biomaterial and how it is analyzed.
Is biomaterial analyzed in your project?
No
Yes (please specify type of material)

Questions from the Project Group Epigenetics & Sequencing

Does your work involve studies of the (epi)genome and/or transcriptome by sequencing methods?
Yes, I conduct experimental work on this subject.
Yes, I conduct theoretical work on this subject.
No, I am not involved in work on this subject.

Comments

Do you have any comments or suggestions? Please enter here: