Frequently Asked Questions (FAQ)
In any case of encountered errors or arising questions with this website, its tools, and plugins, please don't hesitate to contact Timo Lubitz. However, many problems may be sorted out by having a close look to this troubleshooting page. It enlists several troubles that users had and offers solutions.
How do I make a table file SBtab-compliant?
SBtab tables are normal data tables
(spreadsheets or delimited text files), but to enable an easy
exchange of data, the tables themselves, in particular column
titles, need to respect certain rules. You can make your own table
files SBtab-compliant by a number of small changes:
- Choose an SBtab table type appropriate for your specific kind of data
(for a list of predefined table types, see the SBtab specification).
- Insert a declaration line (starting with "!!SBtab") as the first line
of your table and declare the table type by an attribute "TableType='x'"
in the same line, where 'x' corresponds to a valid table type.
- You will also need to set a table identifier by adding the attribute
"TableID='y'" to the first line as well, where 'y' is an arbitrary
identifier (which must be unique for each table in a SBtab document
consisting of more than one table).
- Unique identifers must be given in a
column "!ID". The elements in this column serve as shortnames,
to be referenced in other tables, and must therefore be unique
(e.g., unique gene names). It is good practise to make the "!ID"
column the first column.
Each table type has a predefined set of supported columns, which
can be see in the SBtab specification and
the definitions file. Choose from the list
for your table type, which columns you want to use. Each column
must be preceded with an exclamation mark "!" and its content
must adhere to the data format given in the definitions file.
- In columns containing biological annotations (e.g., database
identifiers for chemical compounds), use column names as described
in the SBtab specification.
If you want to create a whole SBtab document instead of a single
SBtab table, please make sure to be consistent in the usage of
shortnames and be careful that all IDs are unique within the whole
To check your SBtab files for correct syntax,
use the online validator.
I cannot upload and/or convert my SBML file to SBtab.
The SBML to SBtab converter requires SBML code Level 2, Version 4, or higher. Please make sure that your SBML file has the correct file extension (.xml or .sbml) and if this not helps, consult the online SBML validator to ensure that your file is valid SBML.
My SBtab file cannot be uploaded.
SBtab files can be uploaded as long as they have the right file extension. Possible extensions are .csv, .tsv, .xls. However, if you still cannot upload your SBtab file, please consult the SBtab example files that are provided in the Files Section.
When I open my SBtab file with Excel or LibreOffice, the columns are not separated correctly.
This can happen when the spreadsheet tool does not identify the delimiter of the file correctly. Some version of LibreOffice cannot deal with tsv files; in this case it suffices to rename your file extension from tsv to csv and then it works. In any case, all tools offer the possibility to choose the delimiter for the columns. This happens usually on startup of the software (LibreOffice) or can be chosen via the Text Import Wizard (MS Excel).
My SBtab file cannot be converted to SBML.
Note that not *all* SBtab files can be converted to SBML, they need to contain model structure information. Thus, the conversion requires at least a Reaction or Compound SBtab file. Of course, combinations are feasible, as long as one of these mandatory files is provided. If the conversion still does not work, try and validate the files you are using on the SBtab validator page. If there is no validation warning, but the conversion still does not work, please look at the SBtab example files and consult the specification. Oftentimes, it can be helpful to view the SBtab file with a text editor instead of Excel/Open Office; this enables the user to see the file completely unformatted and identify possible problems.
The Excel add-in cannot be installed properly.
This can have several reasons. First, verify that all required pre-requisites are fulfilled for the add-in to work (see add-in page). Then, in Excel you can edit the "SBtab settings" in the SBtab add-in menu. Click the button and make sure that the paths are set correctly: the Python interpreter should be set to the installation directory "xlSBtab/python/python.exe" and the SBtab path should be set to "xlSBtab/SBtab/scripts". The installation directory xlSBtab can usually be found in "/Program Files/" or "/Program Files (x86)/", depending on your system.
I converted SBtab to SBML, but the SBML is invalid.
During the conversion from SBtab to SBML, kinetic laws from the SBtab file can be converted to SBML code. This is a complex process and the kinetic laws provided by the user are not checked for causality: If the user provides erroneous laws, the resulting SBML file will be invalid. The same scenario holds for rules (algebraic, rate, or assignment). In future, SBtab will also comprise validity checks of kinetic laws and rules in SBtabs, but currently this is not the case. By using the SBML online validator, you can always find out which other invalidities an SBML file might hold.
There seems to be a chaos in the submitted SBtab and SBML files in my browser session.
This can happen from time to time while extensive uploading and downloading of files from the server side. Simply click on this clear link to clear all files from your current session and start new.