help:faq [2010/08/24 12:02]
hpm (172.22.10.43) |
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 ===== |
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| | + | 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: |
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| | + | * 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 (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. 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 === |
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| | + | 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. |
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| | + | === 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. | + | |
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| | + | 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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