RDMLedit allows viewing, editing, merging and creating files in RDML format.

GUI consists of five tabs:

• Files: basic file operations:
  • import data (different file formats supported),
  • merge several files into one,
  • review structure of files,
  • save RDML file.
• Metadata: modifications of RDML metadata (e.g., informations about experimenter, samples, targets).
• qPCR: raw qPCR curve data.
• Melting: raw melting curve data.
• Help: this very page.

Files

Upload file(s)

Upload one or more files. Supported formats:

• .rdml or .lc96p – RDML files generated by Bio-Rad CFX96, Roche LightCycler 96 and Applied Biosystems StepOne.
• .csv – file that contains first column cyc for qPCR data or tmp for melting data. Other columns – fluorescence signal. Column names become sample names.
• .xls – file generated by ABI 7500 v.2 software which contains and sheets. To do this use File>Export…; check Sample Setup and Multicomponent Data; select One File; click Start Export.
• .xlsx – file containing description sheet and qPCR data located in adp and/or mdp sheet.

Example structure of sheets in .xslx file:

description

Contains description of experiments. Column names have to be exactly the same as in the example.

fdata.name	exp.id	run.id	react.id	sample	target	target.dyeId
D1	exp1	run1	1	D1 - Stock cDNA	MLC-2v	Cy5
D2	exp1	run2	1	D2 - 1/10 cDNA	MLC-2v	Cy5
D3	exp1	run3	1	D3 - 1/100 cDNA	MLC-2v	Cy5

adp

Contains qPCR fluorescence data. Column names link to the fdata.name at description.

cyc	D1	D2	D3
1	0.1460399771	0.1479223401	0.1474461126
2	0.1520586393	0.1482665679	0.147808717
3	0.1513144293	0.1489176364	0.1483215208
4	0.1525136885	0.1493655183	0.1487343487
5	0.1539632217	0.150546809	0.1490988961

mdp

Contains melting fluorescence data. Column names link to the fdata.name at description.

tmp	D1	D2	D3
20	3401	3595	3656
21	3388	3575	3634
22	3374	3555	3613
23	3361	3535	3592
24	3348	3515	3570

View File

Uploaded file(s) can be viewed by selecting its name at View File selector. After this dendrogram with file structure should appear at the bottom of the page.

Merge RDMLs

You can merge several RDML files into one by selecting RDMLs in Merge RDMLs field. Selected RDMLs will be merged into RDML selected in View File selector. Click Merge to proceed merging.

Date Made and Date Updated

RDML metadata fields.

Remove RDML

Removes uploaded RDML file.

Update

Saves all changes made to RDML. Click this button before downloading edited file!!!

Download RDML

Download currently selected RDML object as compressed RDML v1.2 file.

Metadata

Description of metadata fields can be found in RDML v1.2 format description or in the RDML package help to corresponding classes. Input to any field is validated by RDML classes. For example you cannot input text where number is needed. All errors print to the log at the bottom of the page.

All list elements (i.e. Sample) can be selected by corresponding selector. A new element can be added by writing its name in selector. To remove element, click Remove … at the bottom of the list element editor.

qPCR

Access raw qPCR curves. To view one (or more) curve, click on curve at the table with curves description. To view all curves again – deselect descriptions. Curves arn’t preprocessed and editable!

Melting

Access raw melting curves. To view one (or more) curve, click on curve at the table with curves description. To view all curves again – deselect descriptions. Curves are not preprocessed or editable!