help:faq [2010/02/10 12:17]
hpm (172.22.10.43) Update links to tutorials. |
help:faq [2013/08/21 11:06] (current)
hpm (172.22.68.212) |
| - | ====== FAQ ====== | + | ====== Frequently Asked Questions (FAQ) ====== |
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| | Answers to frequently asked questions (FAQs) about the Web Services provided by EMBL-EBI. | | Answers to frequently asked questions (FAQs) about the Web Services provided by EMBL-EBI. |
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| - | If you have a question that is not answered here please contact [[http://www.ebi.ac.uk/support/index.php?query=WebServices|EBI Support]]. | + | If you have a question that is not answered here please contact [[http://www.ebi.ac.uk/support/index.php?query=WebServices|EMBL-EBI Support]]. |
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| | + | ===== Staying Informed ===== |
| | + | |
| | + | To stay informed about updates and changes to the EMBL-EBI Web Services, and scheduled maintenance to the EMBL-EBI website and services we suggest: |
| | + | |
| | + | * Keep an eye on the [[:about:news|Web Services News]] ([[http://www.ebi.ac.uk/Tools/webservices/feed.php?linkto=current&mode=list&ns=about&type=rss2|RSS]] or [[http://www.ebi.ac.uk/Tools/webservices/feed.php?linkto=current&mode=list&ns=about&type=atom1|Atom]]). |
| | + | * Subscribe to the [[http://listserver.ebi.ac.uk/mailman/listinfo/ws-users|ws-users mailing list]]. This is a low volume mailing list containing service announcements and notification of appropriate training events. |
| | + | * Follow [[https://twitter.com/#!/emblebi|emblebi]] and/or [[https://twitter.com/#!/emblebies|emblebies]] on [[http://twitter.com/|Twitter]]. |
| | + | * "Like" [[http://www.facebook.com/EMBLEBI|EMBL-EBI]] on [[http://www.facebook.com/|Facebook]]. |
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| | ===== How do I use these services? ===== | | ===== How do I use these services? ===== |
| | === Client Development === | | === Client Development === |
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| - | If you want to develop you own clients to the [[:|EMBL-EBI Web Services]], then you will need to set-up an appropriate development environment for your chosen programming language and select an appropriate REST or SOAP library. | + | If you want to develop you own clients to the [[:|EMBL-EBI Web Services]], then you will need to set-up an appropriate development environment for your chosen programming language and select an appropriate REST or SOAP took-kit. |
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| - | A number of [[:tutorials:06_Programming|tutorials]] are provided covering most common programming languages: | + | A number of [[:tutorials:06_Programming|tutorials]] are provided covering most common programming languages and popular tool-kits: |
| | * [[:tutorials:06_Programming:C_CPP|C/C++]] | | * [[:tutorials:06_Programming:C_CPP|C/C++]] |
| | * [[:tutorials:06_Programming:dot_net:Csharp|C#]] | | * [[:tutorials:06_Programming:dot_net:Csharp|C#]] |
| | === Existing Clients === | | === Existing Clients === |
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| - | If you want to download a client and use the service right away then see the clients pages for the service of interest ([[:|list]]). The clients page (e.g. [[clients:interproscan|InterProScan Clients]]) provides a list of clients and details of the pre-requisites. | + | If you want to download a client and use the service right away then see the service documentation pages for the service of interest ([[:|list]]). The service page (e.g. [[:services:pfa:iprscan_soap|InterProScan (SOAP)]]) provides a list of clients and details of the pre-requisites. |
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| - | For most services we provide command-line clients for .NET, Java and Perl. For a few selected services a number of other clients are also available (e.g. [[clients:dbfetch|WSDbfetch]]). Which client you want to use depends on the platform. Currently we recommend using: | + | For most services we provide command-line clients for .NET, Java and Perl. For a few selected services a number of other clients are also available, for example: |
| | + | * [[:services:EB-eye]] |
| | + | * [[:services:pfa:iprscan_rest|InterProScan (REST)]] |
| | + | * [[:services:pfa:iprscan_soap|InterProScan (SOAP)]] |
| | + | * [[:services:sss:NCBI BLAST (REST)]] |
| | + | * [[:services:sss:NCBI BLAST (SOAP)]] |
| | + | * [[:services:dbfetch_rest|WSDbfetch (REST)]] |
| | + | * [[:services:dbfetch|WSDbfetch (SOAP)]] |
| | + | Which client you want to use depends on the platform. Currently we recommend using: |
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| | * MS Windows | | * MS Windows |
| | ===== How can I analyse multiple sequences? ===== | | ===== How can I analyse multiple sequences? ===== |
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| - | The Web Services provided by EMBL-EBI are limited to one sequence, or one set of sequences, per job. Thus if you wish to analyse multiple sequences you will have to submit multiple jobs. The simplest way to do this is to create a set of files containing one sequence per file, and then loop over the files submitting each one, and getting the result. | + | The Web Services provided by EMBL-EBI are limited to one sequence (e.g. the query sequence for a sequence similarity search), or one set of sequences (e.g. the set of sequences to be aligned for a multiple sequence alignment), per job. Thus if you wish to analyse multiple sequences you will have to submit multiple jobs. |
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| - | To split a file containing multiple fasta formatted sequences use the following scripts: | + | **Please note**: We kindly ask all users to submit **NO MORE THAN 25 JOBS AT THE TIME AND NOT TO SUBMIT MORE JOBS UNTIL YOU HAVE OBTAINED RESULTS FOR THE LAST 25**. There are many people using these services and a fair share policy has been implemented that allows us to block users that submit jobs in a manner that prevents others from using the service. This block may affect access to the EMBL-EBI Web Services for an entire organisation or a class B or C subnet. Also make sure you **USE A REAL EMAIL ADDRESS** in your submissions. Using a fake email means we cannot contact you and will very likely result in your jobs being killed and your IP, Organisation or entire domain being black-listed. We do apologise for any inconvenience this may cause. |
| - | * UNIX and UNIX-like environments: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/fsplit.sh|fsplit.sh]] | + | |
| - | * MS Windows: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/fsplit.bat|fsplit.bat]] | + | |
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| - | These scripts require the ''csplit'' program. The ''csplit'' program is available as part of the [[http://www.gnu.org/software/coreutils/|GNU coreutils]] package, for MS Windows a pre-complied version is available: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/csplit.zip|csplit.zip]]. | + | === Multiple sequences per-file === |
| | + | |
| | + | For some services the supplied clients support input of multiple sequences in the [[http://www.ebi.ac.uk/2can/tutorials/formats.html#fasta|fasta sequence format]]. This has to be specifically enabled using a flag, see the client's help/usage information (typically accessed using the ''--help'' option) for details. |
| | + | |
| | + | === File per-sequence === |
| | + | |
| | + | A simple way to do this is to create a set of files containing one sequence per file, and then loop over the files submitting each one, and getting the result. |
| | + | |
| | + | To split a file containing multiple fasta formatted sequences into a set of files each containing a single sequence the following methods can be used: |
| | + | * Use the [[http://emboss.open-bio.org/rel/rel6/apps/seqretsplit.html|EMBOSS seqretsplit]] program, part of [[http://emboss.open-bio.org/|EMBOSS]], a collection of sequence manipulation and analysis tools. |
| | + | * Use a script which uses the ''csplit'' utility. The ''csplit'' program is available as part of the [[http://www.gnu.org/software/coreutils/|GNU coreutils]] package, for MS Windows a pre-complied version is available: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/csplit.zip|csplit.zip]]. See the following scripts for example usage: |
| | + | * UNIX and UNIX-like environments: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/fsplit.sh|fsplit.sh]] |
| | + | * MS Windows: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/fsplit.bat|fsplit.bat]] |
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| | To following scripts illustrate how to submit the jobs: | | To following scripts illustrate how to submit the jobs: |
| - | * UNIX and UNIX-like environments: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/wsbatch.sh|wsbatch.sh]] | + | * UNIX and UNIX-like environments: |
| | + | * Dispatcher: [[http://www.ebi.ac.uk/Tools/webservices/downloads/util/wsbatch.sh|wsbatch.sh]] |
| | + | * JDispatcher: [[http://www.ebi.ac.uk/Tools/webservices/download_clients/util/jdispatcher_file_per-sequence_batch.sh|jdispatcher_file_per-sequence_batch.sh]] |
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| | + | The following parallel job running tools may also be useful: |
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| | + | * [[http://www.gnu.org/software/make/|GNU make]] |
| | + | * [[http://www.gnu.org/software/parallel/|GNU Parallel]] |
| | + | * [[http://www.maier-komor.de/xjobs.html|xjobs]] |
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| | + | === Workflow systems === |
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| | + | Workflow systems (e.g. [[https://kepler-project.org/|Kepler]], [[http://www.taverna.org.uk/|Taverna]] or [[http://www.trianacode.org/|Triana]]) support a number of forms of automated bulk analysis. See [[http://www.ebi.ac.uk/Tools/webservices/tutorials/07_workflows|Workflows and Web Services]] for further details. |
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| | + | === Dedicated Tools === |
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| | + | Dedicated analysis tools, such as [[http://www.blast2go.com/|Blast2GO]], may also use web services to provide some functionality or to perform a specific analysis. See their documentation for details. |
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| | ===== How do I specify a proxy? ===== | | ===== How do I specify a proxy? ===== |
| | ===== Why do you need my e-mail address? ===== | | ===== Why do you need my e-mail address? ===== |
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| - | We require a valid e-mail address so we can contact you in the event of problems with the service which affect your jobs. As described in our [[http://www.ebi.ac.uk/Information/termsofuse.html|Terms of Use]] this information is not provided to anyone else, nor will we contact you except for the reasons stated above. | + | We require a valid e-mail address so we can contact you in the event of: |
| - | | + | * Problems with the service which affect your jobs. |
| - | If you use a fake e-mail address then we will not be able to contact you and will very likely result in your jobs being killed and your IP, Organisation or entire domain being black-listed. | + | * Scheduled maintenance which affects services you are using. |
| - | | + | * Deprecation and retirement of a service you are using. |
| - | ===== Staying Informed ===== | + | As described in our [[http://www.ebi.ac.uk/about/terms-of-use|Terms of Use]] this information is not provided to anyone else, nor will we contact you except for the reasons stated above. |
| - | | + | |
| - | To stay informed about changes to the EMBL-EBI web services and scheduled maintenance we recommend: | + | |
| - | | + | |
| - | - Keep an eye on the [[:about:news|News page]]. There are RSS news feeds associated with the page if you want to see changes in your news reader. | + | |
| - | - The [[http://listserver.ebi.ac.uk/mailman/listinfo/ws-users|ws-users mailing list]]. This is a low volume mailing list containing service announcements and notification of appropriate training events. | + | |
| | | | |
| | + | If you use a fake e-mail address then we will not be able to contact you and will very likely result in your jobs being killed and your IP, Organisation or entire domain being black-listed, see [[http://www.ebi.ac.uk/about/terms-of-use|Terms of Use]]. |
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