FAQ

Sequence Data

 

After a project has been created sequence data needs to be uploaded. At the moment, the only sequence data format we support is DNA FASTA. Files may be compressed using GZIP.

 

Each uploaded sequence requires a unique identifier.

This identifier must be unique across all files uploaded to the same project and is created from the first 70 characters, up to the first space, of the FASTA header.

 

Example FASTA header:

>AC34324 Bacteris

The identifier created from the above FASTA header is "AC34325".

 

SILVAngs supports to upload multiple files at the same time by selecting multiple files in the file selection dialogue or per drag and drop from a file manager, usually holding the SHIFT or CONTROL keys while selecting files.

 

The upload widget, located in the navigation bar right of the main menu, can be opened by a click. The dialogue displays an overview of all files that were chosen for upload and their current status. Using the detail button shows detailed information about the upload.

 

Failed uploads can have the following reasons:

  1. another file with the same name, ignoring the case of characters, already exists in the project,
  2. a file with identical content (both sequence data and headers) already exist in the project, or
  3. the file is not a valid FASTA file, click the details button to see detailed error messages.

 

Additionally, connection errors may occur when if large files are uploaded, we occasionally experience problems when users try to upload files larger than 500 MB. To reduce the file size try to compress the file using GZIP.

 

Also, the credit system limits the overall size of projects that may be analysed free of charge.

 

The credit charge of a project is calculated based on the total number of nucleotides in each sequence file divided by 1.000 (see 'Credit System' in the FAQ for more details).

Project Sharing

 

Every project can be shared by the creator (owner) with other registered users. In the project permission view the email of the user the project should be shared with, has to be added. There is no proof that the email is correct or does already exist in the SILVAngs system. No notification is send.

 

All projects that are shared with you are listed on the "Shared Project" page.

 

The permission “readonly” makes other users able to see your sequence data, parameters and results. Also “readonly” granted users can download the sequence data of your project.

 

The permission “write” allows other users to upload additional data, change project parameters and finally execute projects by using their credits (see credits system).

Credit System

  1. Academic users are granted with 300.000 credits while registration, non-academic get 10.000.
  2. The credit charge will be withdrawn from the account of the users when executing projects.
  3. In case your project needs more credits than available in your account, the project can not be executed.
  4. Every 7 days 50.000 credits will be automatically added to your account with an upper limit of 300.000 credits.
  5. Sharing projects with "write" access gives other users the ability to execute the project with their credits.
  6. If a projects exceeds your maximum credit charge you have the option to request the execution of your project (see Request Project Execution in the FAQ for details). We may choose to contact you if your project greatly exceeds your credit limit.

FAQ

Project Execution

 

Executing an project will lock the project and queue it in the SILVA execution process.

 

The execution time of projects depends on the amount of sequence data, the type of sequence data, the workload of our clusters and the general SILVA NGS service utilization.

 

You and all users the project is shared with are notified by email when the execution is finished.

Request Project Execution

 

The project will not be charged to your account. Scheduling will be done based on the availability of compute time. Please be aware that it can take several days until your project is processed. We reserve the right to deny the execution of large-scale projects.

Regular Expression

 

A regular expression is a string describing a search pattern that is used to search for all possible matching strings in a text or it can be used to match strings.

 

For example the regular expression h[ea]llo world matches both strings hello world and hallo world.

 

More complex patterns can be written using the following operators:

 

Operator Effect
. Matches any single character.
? The preceding item is optional and will be matched, at most, once.
/* The preceding item will be matched zero or more times.
+ The preceding item will be matched one or more times.
{N} The preceding item is matched exactly N times.
{N,} The preceding item is matched N or more times.
^ Matches the empty string at the beginning of a line; also represents the characters not in the range of a list.
$ Matches the empty string at the end of a line.
[abc] Or list, one of the characters in the list.
| Alternation, either the characters on the left side or on the right side.

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Examples:
Sample [12] matches 'Sample 1', 'Sample 2', and 'Sample 11', ...
Sample [123]$ matches 'Sample 1', 'Sample 2', and 'Sample 3', note the use of $ to express that the expression matches until the end of the string.
Sample [^12] matches any sample except 'Sample 1', 'Sample 11', 'Sample 2', ...
Sample [^12]$ matches any sample except 'Sample 1' and 'Sample 2', again the expression must match until the end of the string
Sample 1? matches 'Sample 1', and 'Sample 10' through 'Sample 19'
Sample 1* matches 'Sample 1', 'Sample 10', and 'Sample 11', through 'Sample 111', and all other samples starting with 'Sample 1'.
Acetothermia|Chlorobi matches Acetothermia and Chlorobi
(Alpha|Beta)proteobacteria matches Alphaproteobacteria and Betaproteobacteria
Candidate division (OP3|SR3) matches Candidate division OP3 and Candidate division SR3