Channelpedia

FAQ

Frequently Asked Questions

General

Who maintains and supports Channelpedia ?

Does Channelpedia have a long-term plan ?

What about the ion channels with no data available in Channelpedia ? Is there a plan?

Who can edit Channelpedia? Can I add ion channel informations?

All registered users can edit the wiki-like sections, just clicking on Edit at the top-right of each sub-section.

Who can I contact for more details on the automated patchclamping method?

Data sharing

Can I upload my experimental electrophysiology data on Channelpedia ?

Being Channelpedia a freely-accessible information management network for comprehensive ion channel information, we encourage all researchers to share their data through Channelpedia. Please contact us at bbp.channelpedia 'at' epfl.ch.

Is it possible to download a whole set of ion channel data at once?

Yes, we have an infrastructure suited to share large amount of data. Please contact us at bbp.channelpedia 'at' epfl.ch.

Can I have access to the raw HEKA data files ?

Yes, please contact us at bbp.channelpedia 'at' epfl.ch.

What is the cell ID ?

The cell ID is a unique ID assigned to each cell as soon as it is recorded; it is the main reference to relate every file and every image which is produced from a certain cell.

Ion channels and cell lines

What are the host cell lines ?

What is transcriptome data on cell lines ?

What is a cell line datasheet ?

Are cell lines available for use ?

Can I propose an experiment with ion channel cell lines ?

Which data are available for human and mouse ion channels?

For human, experimental data are available for Kv1.1, Kv1.4, Kv1.5, Kv1.6, Kv2.1, Kv3.4, Kv6.4, Kv11.1 Kv12.3 ion channels.

For mouse, experimental data are available for Kv1.1, Kv1.4, Kv1.5, Kv1.6, Kv2.1, Kv3.4, Kv6.4, Kv10.1 and Kv12.3 ion channels.

NWB files

What is an NWB file ?

An NWB file is a file implemented in the Hierarchical Data Format (HDF5), containing data following the Neurodata Without Borders: Neurophysiology format. The Neurodata Without Borders: Neurophysiology project aims to develop a unified, extensible, open-source data format for cellular-based neurophysiology data.

Which data are stored in an NWB file?

Each NWB file, which is designed to store data in a self-documenting way, contains all the data related to an experiment. The file can be opened with and HDF5 viewer (e.g. HDFView). In the folder acquisition/timeseries there is a subfolder for each applied stimulus, which contains a subfolder for each repetition, where the dataset of the recordings (data) are stored, along with many other metadata, as the seal and the series resistance (r_series) of the patchclamping. Several other metadata are stored in the general/cell_info folder, as the host_cell and the species of the gene.

hdfview.png

How raw data are converted into NWB files ?

Raw data from HEKA Patchmaster are converted into NWB files through custom C libraries (available upon request).

How can I plot the ion channel data?

You can plot ion channel data directly with HDFview, or you can use our API for more elaborated plots.

Analysis

Which programming languages are supported for plotting ion channel electrophysiology data?

We provide API for Matlab and Python. If you prefer another programming language, please contact us at bbp.channelpedia 'at' epfl.ch.

Which are the criteria to define good/bad recordings?

The criteria to define a good recording are based on 6 parameters, whose values have to be within an empirically-determined range:

  • Activity index between 0.3 and 1
  • Voltage offset between -15 and 35 mV
  • Seal larger than 200 MΩ
  • Series resistance smaller than 15.5 MΩ
  • Slow capacitance smaller than 35 pF
  • Maximal current larger than 0.5 nA

What is the Activity Index ?

Are ion channel models available?

Ion channel models will be soon available for Kv channels.