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| Go to one of the Babase [:BabaseWikiAdminGroup:administrators] and ask for access. They will ask [:KarlPinc:Karl] or [:HunterMatthews:Hunter] to make you a username, so pick out the username you'd like. Typically Karl will create the Babase account that grants access to the database itself. Although it is not necessary it is often useful to have a Unix account on [:Papio:papio]. Hunter is the only one that can do this. | === Sign up === Go to one of the Babase [[BabaseWikiAdminGroup|administrators]] ([[mailto:jacob.gordon@duke.edu|Jake]] or [[mailto:wwilber@nd.edu|Willi]]) and ask for access. You will need a Duke NetID; if you are not already at Duke, Jake will sponsor you for a guest account. In addition, it is not necessary but can be useful to have a Unix account on [[Papio|papio]] depending on what type of work you will be doing. Jake can do this for you. |
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| While your at it, it's a good idea to sign up on the [:BabaseMailingLists:Babase mailing lists], and get yourself a login on this wiki as well. | While you're at it, it's important to sign up on the [[BabaseMailingLists|Babase mailing list]] and a good idea to [[TheBabaseWiki|get yourself a login]] on this wiki as well. |
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| Yes, there are a lot of logins to keep track of. Each person has a login to the database, and possibly a Unix login on Papio, a login on this wiki, and an email address and password used to sign up for the mailing lists. All of these are different logins, with, possibly but not necessarily, different usernames and different passwords. | Yes, there are a lot of logins to keep track of. Each person has a Duke NetID, a login to the database, a login on this wiki, and an email address and password used to sign up for the mailing list. All of these are different logins, with, possibly but not necessarily, different usernames and different passwords. |
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| Queries, written in the SQL query langage, are used to obtain data from the database. It is highly recommended that users begin by reading the [http://www.postgresql.org/docs/8.1/static/tutorial-sql.html tuitorial] on the SQL language found in the [http://www.postgresql.org PostgreSQL] [http://www.postgresql.org/docs/8.1/static/index.html documentation]. Someday this wiki may have a short tuitorial using the Babase data itself, but there isn't one now so if you want to start one please go ahead. Meanwhile, try out some queries in the Babase [https://papio.biology.duke.edu/phpPgAdmin/ phpPgAdmin web interface] by clicking on the "SQL" link in the upper right hand corner after logging in and choosing the babase database, babase schema. To find your way around the various Babase databases read the Babase [http://papio.biology.duke.edu/babase_system_html technical documentation]'s sections on the [http://papio.biology.duke.edu/babase_system_html/ch02s01.html Babase databases] and [http://papio.biology.duke.edu/babase_system_html/ch02s02.html schemas]. | === Tour Babase === |
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| Unfortuneately, at the present time downloading the results of a query requires the results be saved in a table. Each Babase user has his own area of the database, called a schema, where they can create their own tables. To save the results of a query into a table, "newtable", in your schema, add "INTO yourlogin.newtable" to your SQL query, as documented in the [http://www.postgresql.org/docs/8.1/static/sql-selectinto.html SELECT INTO] documentation. The phpPgAdmin web interface can then transfer the contents of your new table to your desktop. Go into your schema, the one named with your database login, and click on the "newtable" table you just created. Click on the "Export" link at the upper right. Choose "Data Only" and a format of either "CSV" or "Tabbed" if you wish to use the data in Excel later. | '''This section is out of date and needs to be updated. Someday.''' |
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| The sections of the PostgreSQL documentation of initial interest are: | Download and follow the document [[attachment:Getting_Started.pdf]] It will guide you through the basics of navigating the PPA interface and show you how to browse Babase tables and views. Some of the content is old, e.g. the suggestion to use Mozilla Sea Monkey instead of Internet Explorer. The ''core'' content is still true, however. |
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| * section I [http://www.postgresql.org/docs/8.1/static/tutorial.html Tuitorial] * subsection I.2 [http://www.postgresql.org/docs/8.1/static/tutorial-sql.html The SQL Language] * section II [http://www.postgresql.org/docs/8.1/static/sql.html The SQL Language] * section VI [http://www.postgresql.org/docs/8.1/static/reference.html Reference] * subsectin VI.I [http://www.postgresql.org/docs/8.1/static/sql-commands.html SQL Commands] |
=== Write Queries === Queries, written in the SQL query langage, are used to obtain data from the database. It is highly recommended that users begin by reading [[SQL_Language|Babase's SQL tutorial]]. The [[http://www.postgresql.org/docs/current/tutorial-sql.html|tutorial]] on the SQL language found in the [[http://www.postgresql.org|PostgreSQL]] [[http://www.postgresql.org/docs/current/index.html|documentation]] may also be helpful. As you read, try out some queries in the Babase [[https://papio.biology.duke.edu/phpPgAdmin/|phpPgAdmin web interface]] by clicking on the "SQL" link in the upper right hand corner after logging in and choosing the babase database, babase schema. You should also try writing queries using our specialized [[SQL_Program|SQL program]]. === Download Babase data for further analysis === Downloading the results of a query can be done by clicking the Download option at the bottom of the page where your query return appears. The results can also be saved in a table. Babase users each have their own area of the database, called a schema, where they can create their own tables. To save the results of a query into a table, "newtable", in your schema, add "INTO yourlogin.newtable" to your SQL query, as documented in the [[http://www.postgresql.org/docs/current/sql-selectinto.html|SELECT INTO]] documentation. The phpPgAdmin web interface can then transfer the contents of your new table to your desktop. Go into your schema, the one named with your database login, and click on the "newtable" table you just created. Click on the "Export" link at the upper right. Choose "Data Only" and a format of either "CSV" or "Tabbed" if you wish to use the data in Excel later. === Learn more === The sections of the PostgreSQL documentation of initial interest are as follows: * section I [[http://www.postgresql.org/docs/current/tutorial.html|Tutorial]] * subsection I.2 [[http://www.postgresql.org/docs/current/tutorial-sql.html|The SQL Language]] * section II [[http://www.postgresql.org/docs/current/sql.html|The SQL Language]] * section VI [[http://www.postgresql.org/docs/current/reference.html|Reference]] * subsection VI.I [[http://www.postgresql.org/docs/current/sql-commands.html|SQL Commands]] More resources can be found on the BabaseHelp page. |
Sign up
Go to one of the Babase administrators (Jake or Willi) and ask for access. You will need a Duke NetID; if you are not already at Duke, Jake will sponsor you for a guest account. In addition, it is not necessary but can be useful to have a Unix account on papio depending on what type of work you will be doing. Jake can do this for you.
While you're at it, it's important to sign up on the Babase mailing list and a good idea to get yourself a login on this wiki as well.
Yes, there are a lot of logins to keep track of. Each person has a Duke NetID, a login to the database, a login on this wiki, and an email address and password used to sign up for the mailing list. All of these are different logins, with, possibly but not necessarily, different usernames and different passwords.
Tour Babase
This section is out of date and needs to be updated. Someday.
Download and follow the document Getting_Started.pdf It will guide you through the basics of navigating the PPA interface and show you how to browse Babase tables and views. Some of the content is old, e.g. the suggestion to use Mozilla Sea Monkey instead of Internet Explorer. The core content is still true, however.
Write Queries
Queries, written in the SQL query langage, are used to obtain data from the database. It is highly recommended that users begin by reading Babase's SQL tutorial. The tutorial on the SQL language found in the PostgreSQL documentation may also be helpful. As you read, try out some queries in the Babase phpPgAdmin web interface by clicking on the "SQL" link in the upper right hand corner after logging in and choosing the babase database, babase schema. You should also try writing queries using our specialized SQL program.
Download Babase data for further analysis
Downloading the results of a query can be done by clicking the Download option at the bottom of the page where your query return appears. The results can also be saved in a table. Babase users each have their own area of the database, called a schema, where they can create their own tables. To save the results of a query into a table, "newtable", in your schema, add "INTO yourlogin.newtable" to your SQL query, as documented in the SELECT INTO documentation. The phpPgAdmin web interface can then transfer the contents of your new table to your desktop. Go into your schema, the one named with your database login, and click on the "newtable" table you just created. Click on the "Export" link at the upper right. Choose "Data Only" and a format of either "CSV" or "Tabbed" if you wish to use the data in Excel later.
Learn more
The sections of the PostgreSQL documentation of initial interest are as follows:
section I Tutorial
subsection I.2 The SQL Language
section II The SQL Language
section VI Reference
subsection VI.I SQL Commands
More resources can be found on the BabaseHelp page.