For the following products FAQs are available. Please click on the specific product you are interested in:
FAQs for bioSCOUT
Q1. How can I move one or more analyses from one project to another?
This is not possible in bioSCOUT, please re-run this task in the new project and delete the old analysis in the former project.
Q2. How can I update my analysis?
Go to the Completed Tasks section and start a new Automated bioSCOUT annotation.
Q3. How can I create a new Project in bioSCOUT?
If you have the right to administer project groups, click the Admin button on the top the Analysis Hierarchy and refer to point 2. Project Group Management.
Q4. Where can I get my bioSCOUT Interactive Task results?
You can open the result page by clicking on the respective link in the Completed Tasks section.
Q5. How can I start Multiple Sequence Alignments out of my results of an annotation?
1. Use a Blast link from the Homologies section in the feature report.
2. Click on the table link on the next page.
3. Select the blast hits you need to compare.
4. Start a new task with the New Tasks button on the top or the bottom of the list.
5. Select the tool you want to use and press OK on the bottom of the page.
Q6. How can I change parameters e.g. Blast scoring matrix etc.?
Start a new Interactive task in the Feature Page, select a tool and check the specify tool parameters checkbox before launching the task with the OK button. In the next window you can change parameters for the selected tool.
Q7. How can I start a new analysis or a task out of SRS?
Enter the SRS within bioSCOUT with the SRS button on the top of your Analysis Hierarchy. Find and select the sequence(s) you need and press the New Analyses button on the left side to launch your task in bioSCOUT.
Q8. How can I integrate my Alert results into my Feature Report?
Just restart the analysis.
Q9. What does the Update button at the top of the page mean?
With this Update mechanism you can import results of interactive tasks in to the Feature Report.
Q10. How can I delete my Alert Jobs?
First inactivate these Alert jobs, and then delete them.
Q11. Why do I miss some tool in the Tool Selector Page?
The Tool Selector Page only shows you tools, which you are able to use with the set and the type of sequences you have selected.
Q12. Can I group single analyses?
Yes, select the analyses you want to group in the Analysis Hierarchy Page and go to the bottom of this page. Here you can reorganize selected analyses by attaching them to an existing analysis or joining them to a new analysis.
Q13. How can I share my analysis?
Click on the button located on the right of the permissions section of the feature report for your analysis. Then modify the permissions as desired and click ok.
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Database Update System (DUS) for bioSCOUT
Part 1: General questions
Q1.1. What is the difference between the former "DBUpdate" and the new Database Updating System ?
The former DBUpdate had several disadvantages. , e.g. the recovery mechanism after a ftp crash was not good. There are too many dependencies in creating e.g. NRDBs, as soon as one step failed the entire process came to a stand still. The former DBUpdate used too much cpu, and it was relatively slow. Furthermore, the results of the ftp and indexing process were not visualized in a user-friendly way.
The new Database Updating System is:
easier to maintain
uses less memory (~10-fold during NRDB creation)
In short, the customer will gain time and needs less memory.
Part 2: Questions regarding installation
Q2.1. What are the system requirements for bioSCOUT 1.6/DUS?
2.5 TB disk space (NFS or local), large file support (files >2GB),
250 GB disk space (local), large file support (files >2GB),
4-8 CPUs (total 3-4GHz)
10GB Swap space
Network bandwidth 1GB FTP/day
DLT IV tape drive for initial databank installation
SRS 7.0 and SRS Prisma 3.0 (or better)
Q2.2. Why has the swap space requirements decreased?
The creation of non-redundant databases have been rewritten. These tasks now use considerably less memory than before. The maximum memory requirements are now expected with SRS indexing, e.g. building links between large major databases or NRDB indexing (~10GB).
Q2.3. Why is a local disk required?
As NRDB creation now has rather low memory demands, it now relies on very fast disk I/O for reading and writing (temporary) files. NFS filesystems are too slow for this task. Therefore, the NRDB files, blast indices, SRS indices and source FASTA databases should be on a local partition with e.g. a fiber channel access.
Q2.4. Can I reuse the dbUpdate 5 configuration?
No. Although the syntax of configuration files of dbUpdate 5 remained largely the same, these files should not be used anymore. They contain now unused settings,the locations of the various update scripts have changed and they cannot be maintained in a modular manner. Furthermore, the FTP configuration has moved into Prisma Resource files (*.it). So, you should use the configuration delivered with DUS and adapt them with respect to additional databanks managed with dbUpdate 5.
Q2.5. Does DUS needs any other applications or parts of dbUpdate 5?
No. DUS is mostly self-contained. It needs some standard Unix system commands and uses bioSCOUT components only for starting the Alert server. As soon as DUS runs smoothly, you may delete or reuse all dbUpdate 5 directories/files, namely
Q2.6. Can DUS be used with bioSCOUT 1.5.3?
No. DUS was tested with SRS 7.0/Prisma 3.0 only, while bioSCOUT 1.5.3 was not.
Q2.7. Can dbUpdate 5 be used with bioSCOUT 1.6?
No. bioSCOUT 1.6 needs SRS 7.0, which is not supported by dbUpdate.
Part 3: Questions regarding general DUS configuration
Q3.1. How can I add a database to DUS to be regularly updated?
Please refer to the corresponding section in the „Configuring DUS“ manual. Make sure you have solid knowledge of how SRS and DUS works before you do this. When in doubt, contact LION.
Q3.2. Does DUS supports load balancing systems?
DUS itself has no built-in support for load balancing systems yet, this will probably be included in the next DUS release. However, the dbupdate.csh starter script can be submitted to a load balance system, so that the complete task runs inside this system.
Q3.3. Where did the „manual“ jobs of dbUpdate 5 go?
There is no more need for manual jobs. DUS is capable of handling large major databanks automatically, too.
Part 4: Questions regarding Downloading tasks
Q4.1. Can FTP servers be accessed via a proxy?
Yes, set the FTP_PROXY variable in the $DB_UPDATE/update_env.csh file accordingly. You can also include user and password information, if required, e.g.:
setenv FTP_PROXY http://user:firstname.lastname@example.org:8080
Q4.2. Can FTP servers be accessed via a firewall, that only allows for passive mode FTP sessions?
Yes, turn on passive mode in /LION/sysiphus/pubgen/etc/wgetrc
Q4.3. Can FTP bandwidth be reduced during work hours?
No. The underlying FTP tool wget doesn't support any limitation of used network bandwidth. An alternative would be to reschedule FTP tasks, so that they are executed less frequently or at night or weekends. However, they should not overlap with data preparation tasks, so one has to adapt their schedule as well.
Q4.4. Can I deny downloading an updated databank?
Some large databanks are updated quite frequently, however, the changes are not worth the long download time. A prominent example is the bi-weekly updated dbEST (Release) with its data volume of about 30GB.
DUS does not yet offer a setting that prevents downloading updated data (e.g. „decline downloads until the data has been updated three times“). You have either to comment the corresponding lines in the weekday list file or reduce the number of FTP tasks in the crontab schedule.
Part 5: Questions regarding data preparation
Q5.1. The PrismaView facility sometimes needs a long time to display the graphics or issues an error message. Why is that?
Probably Prisma re-indexes the data needed for this graphics display. With large SRS installations, this may take up to several minutes. This is a known defienecy and is being addressed in future releases.
Q5.2. How can I keep the SRS databanks stable for some time but continue downloading?
Simply deactivate the Update list tasks in the crontab.
Q5.3. How can I keep a certain SRS databank stable for some time?
If you want to continue downloading new data, put a comment ( # ) character before the corresponding include-statement from the main list, e.g. for GENBANK in the file $DB_UPDATE/DUS_LIST_DD:
You can also stop downloading this databank (see 4.4). As there is no data downloaded anymore, the databank is not going to be indexed.
Q5.4. How can I force a certain update target to be executed?
Put a „Completed“ flag in the $TRACE_DB directory, e.g. for SWISSNEW:
Global targets are only executed if any of the other targets in this list have been successfully executed. If you don’t think this will happen, for whatever reason, you can add a „dummy“ target to the list, e.g.:
Q5.5. Why has my new version of NRNEE (or NREST) so many modified or added entries?
From time to time, the .diff File, which contain the differences between two subsequent NR databank versions, gets very large. This can even cause the incremental assemble step to crash due to exhausted memory.
There are three possibilities for this behavior:
1. A new GENBANK or EMBL release has been indexed. This causes lots of changes in the NR databanks as well. Make sure to set the INCREMENTAL_NR* variables in update_env.csh to „n“ as soon as one of the large databanks have been indexed. The .diff file still will be very large, however, it will not be used to update the existing nonredundant databank.
2. There has been a lot of GENBANKNEW and EMBLNEW updates since the last NR databanks were built. If you update your NR databanks e.g. only twice a month, it is recommended to set the INCREMENTAL_NR* variables in update_env.csh to „n“.
3. Otherwise there might have been a I/O error while reading one of the fingerprint index files. Check whether you are able to read them from the command line (e.g. by counting the lines: wc –l nrest_complete.raw). If you get an error, you probably have to stick to the old version of the non-redundant databank while you are rebuilding it.
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