SeWeR: Customization

SeWeR: SEquence analysis using WEb Resources
Customization page: Add a service
Welcome to customization page of SeWeR! SeWeR is completely customizable now. If a particular program is not offered by SeWeR, by following these simple steps you can add the program to SeWeR seamlessly. The program/service should have a HTML query page. SeWeR will parse the page and will incorporate it. Please note: Netscape on Windows platform is funny when it comes to pasting large amount of data. Some of the SeWeR target pages are bigger than what Netscape can handle on Windows. If SeWeR tells you that the target page is incomplete, then use Internet Explorer. Netscape on Linux (and hopefully on other Unices) doesn't have this problem. Netscape perhaps believes that users on Windows are kids and do not require to handle large data. :-) Step #1 If you are not running this page from your computer then close this page. Download SeWeR. The customization will only work on a local copy of SeWeR as it involves saving pages on your computer. Unzip the archive and open "custom.htm" (this page) in your browser. You can also run SeWeR (opening sewer.htm) and come to this page by following links from the starting page. Step #2 Download/Save the HTML page of the service. Note the page URL. Search for the help page of the program if any, and note that URL. Step #3 Name of the program Must be a single word. e.g. BlockMaker or ClustalW. Step #4 Type the program URL Type the complete URL of the program that you noted down in the first step (you can visit the page and copy and paste the URL here). This will be the link shown in "more" button in the program description. e.g. http://www.ebi.ac.uk/clustalw/. Step #5 Type the help page URL Type the complete URL of the program help page that you noted down in the first step (you can visit the help page and copy and paste the URL here). This will be the page SeWeR will open if you click the "help" button. If you don't have the help page URL, leave this entry blank. SeWeR will use the program URL supplied in the previous step. e.g. http://www.ebi.ac.uk/clustalw/help.html. Step #6 Query type DNA/Protein sequence Keywords Choose the type of query. The query can be of two types- DNA/Protein Sequence or keywords (e.g. PubMed). SeWeR at present can not handle "file upload". If you choose DNA/Protein sequence then SeWeR searches for a <textarea> element as query. If it finds more than one <textarea> element then it will ask for the name of the main query. Otherwise, if there is only one <textarea> element and if you have chosen the query type to be DNA/Protein sequence then it will automatically take the single <textarea> element as the main query. If you have chosen keyword as the query type then you need to supply the name of the main query in Advanced Information section.
Step #7 Type your program description here Type a brief description of the program here. Information like, what it does, what are the mandatory options, limitations etc.
Step #8 Copy and paste the service form Open the service form page in a text editor and copy and paste the whole page here.
Step #9 Copy and paste the SeWeR target page Open the SeWeR target page in a text editor and copy and paste the whole page here. The pages that can be used are- nucleicacid.htm, protein.htm, align.htm, database.htm, pcr.htm, tools.htm. Select the appropriate page, open in a text editor and copy and paste the whole page here. Please Note that you require SeWeR ver 2.5 pages. Also note that Netscape on Windows has a bug that might prevent a large file to be pasted. Some of the SeWeR pages are bigger than what Netscape can handle on Windows. SeWeR will prompt you for full page if it finds the page is incomplete.
SeWeR is now ready to process the form. It will open a new window to process the page. It might even prompt you for some queries. If everything goes well you will find "Preview" section forms are filled up. If it shows some errors then supply additional information in the next section. Otherwise skip the following section.
Advanced Information You need to provide information for this section only when SeWeR shows an error while processing. Additional step #1 Type the query name This is the name of the "query". If your query is DNA/Protein sequence then the query is a <textarea> element. If the "form" has more than one <textarea> element then type in the "name" of the <textarea> of the sequence query. For e.g. <textarea name="sequence"... Type sequence in the query name. If the form has only one <textarea> element and the query is a nucleotide/protein sequence then leave this field blank. SeWeR will take the "name" of the single <textarea> element present in the "form". If the query is anything other than nucleotide/Protein sequence (may be a key-word, like in case of PubMed) then you must provide the name of the corresponding element. For e.g. <input type="text" name="keywords"... Type keywords in the query name. Additional step #2 Which "form" to process? Form # If SeWeR finds more than one <form> element, then supply the form number here. The first <form> will be considered as "form #1", the second one will be "form #2" etc.
Preview To add a service to SeWeR there are five places where HTML code has to be added. For easy addition I call them as Section #1, #2... etc. Each of the section codes can be copied and added manually in the place mentioned. But SeWeR can automatically add the code for you. Before you do that edit each section code as you feel suitable for you. Particularly, preview the option list by pressing the button and replace all the "Type your description here" with the suitable descriptions. You can refer to the original page if required. If you know how to edit HTML you can even modify the default values. When you are satisfied move to the next section. Section #1 This code goes to the place after <!--Section #1 codes goes here-->. Overwrite the line <!--included_programs=".... Section #2 This code goes to the place after /**Section #2 code goes here**/ within the init() function.. Section #3 This code goes to the place after <!--Section #3 codes goes here-->. Section #4 Program Description This code goes to the end of the page before</body> tag. Section #5 Option list This code goes to the end of the page before</body> tag. Before that replace "Type your description here" with your description in the code. Test the look of the option page by clicking on "test option list" button.
Incorporation If you are satisfied with the option page then click the following button. SeWeR will open a new window containing the new page.
Copyright © 2000 Malay Kumar Basu Send your comments/suggestions/bug-report to me: curiouser@ccmb.ap.nic.in Disclaimer