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, these tables 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).
- The second row after the declaration row is the row with
the column titles. Unique identifiers 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.
You can also add individual columns that are not part of the
SBtab predefined table type. If you do so, simply omit the "!"
at the beginning of the column header. Then, the column is part
of your SBtab but its content will be ignored by SBtab software tools.
- 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
document. You will further need to begin your document with a document
declaration row preceded with "!!!SBtab" and followed by the
If you are still unsure about aforementioned points, we suggest you
have a look at our numerous example files in the
In the end, to check your SBtab files for correct syntax,
you can 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 does not help, 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, .xlsx. We recommend the usage of .tsv.
However, if you still cannot upload
your SBtab file, please consult the SBtab example files that are provided in the
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
xlSBtab 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
link to clear all files from your current session and start new. Note that currently
uploaded files will be lost from the session.