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=== Babase Boot Camp === === 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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In order to use the data within Babase, each new user must complete all of the steps of the Babase Boot Camp training program. Through completion of this Boot Camp, you will become one of the few, the proud, the Babase users. Completion of this course is vital to your understanding of the data and the database structure and is therefore mandatory. Please see Niki or Lacey for details before proceeding. 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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=== Sign up ===
Go to one of the Babase [:BabaseWikiAdminGroup:administrators] (Lacey or Niki) and ask for access. They will make you a username, so pick out the username you'd like. In addition, although it is not necessary, it can be useful to have a Unix account on [:Papio:papio] depending on what type of work you will be doing. Ryan Hardy is the only one that can do this. Ask Lacey or Niki to put you in touch with him.		 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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While your at it, it's important to sign up on the [:BabaseMailingLists:Babase mailing lists] and a good idea to [:TheBabaseWiki:get yourself a login] on this wiki as well. === Tour Babase ===
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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. '''This section is out of date and needs to be updated. Someday.'''
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=== Tell Your Browser Papio Is Not Evil ===
When you attempt to use Babase you will often find that
"The computer advises me to cancel everything and not to proceed
with Babase."

Ignore the warnings. The browser is warning you that
Babase has not paid to have it's identity verified. Tell your browser
to ignore the problem, forever.

## This really belongs in a footnote, but we need to wait to upgrade the OS before footnotes become available.
(To clarify, web browsers use certificates to, ostensibly,
secure your web access. These are issued, for a annual
fee, by organizations known as certificate authorities.
They are supposed to assure you that you are interacting
with who you think you are interacting with. In actual fact
"[http://www.crypto.com/blog/spycerts/ Certificate authorities protect you from anyone from whom they are unwilling to take money.]"
The people who verify identities on the web seem
to verify no more than whether or not they've received payment.
The little lock icon your browser shows indicates that someone
who has claimed an identity has paid. The purchaser may
or may not have legitimate title to the purchased name, the
identity may or may not have been stolen, the website on the
far end may or may not take your money without sending you product,
mis-use your credit card number, etc., etc.)

Babase re-generates it's identity once each year, sometime around
April, and at that time everybody has to tell their browser to
permanently accept the new identity so that such warnings are
not displayed.

(Those worried that evildoers are attempting to steal their
Babase password can ask their browser to display the details
of the identity credentials (page info, Ctrl-i in firefox)
and verify that the SHA fingerprint is: 74:78:f6:aa:31:4a:50:75:fb:5a:7d:ed:4c:a9:07:6b:37:f0:6c:73)

=== Tour Babase 2.0 ===
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.		 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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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 tuitorial]. 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] 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. 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]. 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]].
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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. 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.
 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.
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The sections of the PostgreSQL documentation of initial interest are: The sections of the PostgreSQL documentation of initial interest are as follows:
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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]		  * 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]]

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:

More resources can be found on the BabaseHelp page.

GettingStartedWithBabase (last edited 2024-10-28 21:46:58 by JakeGordon)

Wiki content based upon work supported by the National Science Foundation under Grant Nos. 0323553 and 0323596. Any opinions, findings, conclusions or recommendations expressed in this material are those of the wiki contributor(s) and do not necessarily reflect the views of the National Science Foundation.