Screen capture of the Intrepid Bioinformatics website.

Ok, bad paraphrasing aside, for one moment, put on your best “Gordon Gekko” suit, and loosely consider this:

In finance, a portfolio is a collection of investments held by an institution or an individual. Holding a portfolio is a part of an investment and risk-limiting strategy called diversification – by owning several assets, or “things with value”, certain types of risk can be reduced. In building up an investment portfolio, a financial institution will typically conduct investment analysis, while a private individual may make use of a financial advisor/institution’s portfolio management services.

Now ask yourself this – what if there were a way to do this with, oh I don’t know: your genetic data? Enter Intrepid Bioinformatics.

Intrepid’s founders had a vision, one of a heterogenous genetic data management platform that would allow researchers to store, compare, and contextualize genetic trends, as well as purchase reagents and consumables, all in one place. With a newly-designed identity by Katie Bush Design, Inc. in hand, Intrepid and their team came to Mission Data looking to take this concept out of the futuristic conversational realm and bring it into the “now”.

What Does It Do?

A “software-as-a-service” platform allows genetic researchers to compare similar data sets from thousands of samples side-by-side. With Intrepid, a researcher can begin to quickly identify trends in entire populations which will have the potential to quickly advance discoveries in the medical, pharmaceutical and agricultural biotechnology industries. From free trials to rich-access subscriber plans, users are presented with an impressive load of features right out of the gate – multiple upload options, data downloading, user tutorials, and active collaboration between other community members of your choice, to name a few.

Who’s Using It?

Intrepid appeals to the genetic research community in two sectors: human genome research and animal (specifically, bovine) research. The markets for these two segments are vastly different, and the audience can be further segmented into researchers working for larger companies/governments/universities vs. researchers in small, relatively unfunded labs.

Take, for example, a cattle farmer. He or she obviously has a vested interest in ensuring that their clients are receiving the best product possible, be it milk, beef, etc. By using Intrepid’s services, they can access a wealth of genetic data that will help them determine which lines of cattle are best suited for those assorted purposes. And, which lines they might want to avoid because of a predilection for disease.

That’s not to say those are the only audience contingents that Intrepid is looking to pull into their community. On the contrary, a day on the horizon can be seen in which members of the public can look to utilize Intrepid Bioinformatics’ services like a digital genetic bank, safely and securely storing their data with constant and “at-will” access.

Our team at Mission Data constantly look to push and redefine the boundaries of what is thought possible and conventional in the realm of the web. And, I think I can speak for all of us when I say that if we can eliminate boundaries and make the ideas of the future happen while partnering with great clients, then the ride is made all the better. This was certainly the case here.

To further paraphrase Gordon Gekko: “It’s all about the ‘now’, kid. The rest is just conversation.”

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Working with the Tasting Table team, Mission Data designed and developed the iPhone application including integrating with Tasting Table’s web services on their existing web-based application taking the existing website content mobile.

Download the application from the iTunes App Store to find nearby recommendations, create and manage your To-Do lists and consume articles and recommendations from the Tasting Table website easily on your iPhone or iPod touch.

For my example I chose the latter. Quoted-printable has two distinct advantages: 1) It should be supported by all servers and 2) Unlike base64 it will keep characters that are 7bit ascii in ascii and only encode characters it needs to.

CREATE OR REPLACE PROCEDURE MAIL_TEST IS
  lv_server      VARCHAR2(255) := '';
  lv_rcpt        VARCHAR2(255) := 'to@example.com';
  lv_from        VARCHAR2(255) := 'from@example.com';
  lv_subject     VARCHAR2(255) := 'Le chien paresseux a sauté';
  lv_message     VARCHAR2(255) := 'Voix ambiguë d''un coeur qui au zéphyr préfère les jattes de kiwis';
  lv_conn        UTL_SMTP.CONNECTION;
BEGIN
  lv_Conn := UTL_SMTP.Open_Connection(lv_server);
  UTL_SMTP.Helo(lv_conn, lv_server);
  UTL_SMTP.Mail(lv_conn, lv_from);
  UTL_SMTP.Rcpt(lv_conn, lv_rcpt);
  UTL_SMTP.OPEN_DATA(lv_conn);
  UTL_SMTP.WRITE_DATA(lv_conn, 'Subject: =?UTF-8?Q?' ||
                                UTL_RAW.CAST_TO_VARCHAR2(UTL_ENCODE.QUOTED_PRINTABLE_ENCODE(UTL_RAW.CAST_TO_RAW(lv_subject))) ||
                                '?=' || UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn, 'MIME-version: 1.0' || UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn, 'Content-Type: text/html;charset=utf-8' || UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn, 'Content-Transfer-Encoding: quoted-printable '|| UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn, 'Date: ' || TO_CHAR(SYSDATE, 'dd Mon yy hh24:mi:ss' ) ||' -0800 (GMT)' || UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn, 'From: ' || lv_from || UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn, 'To: ' || lv_rcpt || UTL_TCP.CRLF);
  UTL_SMTP.WRITE_DATA(lv_conn,  UTL_TCP.CRLF);
  UTL_SMTP.WRITE_RAW_DATA(lv_conn, UTL_ENCODE.QUOTED_PRINTABLE_ENCODE(UTL_RAW.CAST_TO_RAW(lv_message)));
  UTL_SMTP.WRITE_DATA(lv_conn, UTL_TCP.CRLF);
  UTL_SMTP.CLOSE_DATA(lv_conn);
  UTL_SMTP.QUIT(lv_conn);
END;

If you wanted to use 8bit ascii you would change the data and transfer encoding header to this:

UTL_SMTP.WRITE_DATA(lv_conn, 'Content-Transfer-Encoding: 8bit'|| UTL_TCP.CRLF);
UTL_SMTP.WRITE_RAW_DATA(lv_conn, UTL_RAW.CAST_TO_RAW(UTL_TCP.CRLF || lv_message || UTL_TCP.CRLF));

Finally, you can also use base64 encoding for the subject:

  UTL_SMTP.WRITE_DATA(lv_conn, 'Subject: =?UTF-8?B?' ||
                                UTL_RAW.CAST_TO_VARCHAR2(UTL_ENCODE.BASE64_ENCODE(UTL_RAW.CAST_TO_RAW(lv_subject))) ||
                                '?=' || UTL_TCP.CRLF);

Calling me a PL/SQL developer would be an insult to PL/SQL developers everywhere. I apologize in advance for any perceived lack of style. Most of the variables would be sourced from parameters passed in to the procedure or database values.

SELECT mycol FROM sometable WHERE sometimestamp < "30 seconds ago"

The main trick here is to know that sysdate math is based in days and fractional days work. Here are a few examples:

Remove hours from a date:

sysdate – hours/hours in a day

Remove minutes from a date:

sysdate – minutes/(hours in a day * minutes in an hour)
or
sysdate – minutes/minutes in a day

Remove seconds from a date:

sysdate – seconds/(hours in a day * minutes in an hour * seconds in a minute)
or
sysdate – seconds/seconds in a day

The example above would be:

SELECT mycol FROM sometable WHERE sometimestamp < sysdate - 30/(24*60*60)

sqlplus login/pwd@//hostname:1521/sidname

This should work with versions 9 and above. Let me know if other versions work.

It took a little digging to find out how to convert a epoch style timestamp but here it is:

select new_time( to_date('01011970', 'ddmmyyyy') + 1/24/60/60 * :currenttimeinmillis/1000, 'GMT', 'EDT' ) from dual

Note that I convert the output from GMT to EDT here.

1. Gather the installation sources you will need. You have to be registered with oracle to get their instant client packages.
   Download the ruby oci8 drivers
   Download the oracle instant client
   You want the following packages (these examples assume the zip format):
   • Instant Client Package – Basic or Instant Client Package – Basic Lite
   • Instant Client Package – SDK
   • Instant Client Package – SQL*Plus (optional but nice to have)
2. Install oracle instant client packages
   
   I unzip them in the /opt directory and assume that for the examples. It doesn’t matter where you put them as long as you know where they are.
   
   The zip packages have one problem that needs to be solved after they are expanded. You must create a symlink in the install directory for a shared library: ln -s libclntsh.so.10.1 libclntsh.so
   

3. Set up the oracle environment:
   

   I created a script called oracleenv.sh with the following lines in it:

        export ORACLE_HOME=/opt/instantclient_10_2/
        export LD_LIBRARY_PATH=/opt/instantclient_10_2/
        export PATH=/opt/instantclient_10_2/:$PATH
        export SQLPATH=/opt/instantclient_10_2/
        export TNS_ADMIN=/etc/
   

   and then I source it when I want to use something oracle related “. oracleenv.sh”. You may want to just put it in your profile.
   

   You also need to create a /etc/tnsnames.ora file. This can be tricky. The best option is probably to ask your DBA to create it for you. Here is an example:
   

   DEVDB.WORLD =
     (DESCRIPTION =
       (ADDRESS_LIST =
           (ADDRESS =
             (COMMUNITY = tcp.world )
             (PROTOCOL = TCP)
             (Host = 192.168.1.125)
             (Port = 1546)
           )
       )
       (CONNECT_DATA = (SID = DEVDB)
       )
     )
   

   The main thing you need for ruby later is the SID. At this point you may want to try to use sqlplus to see if you can connect to the database.

4. Build the ruby oci8 package
   
   untar

   ruby setup.rb config -- --with-instant-client=/opt/instantclient_10_2/

   make
   make install

5. Give the low level API a test
   

   ruby -r oci8 -e "OCI8.new('username', 'password', 'DEVDB.WORLD').exec('select sysdate from dual') do |r| puts r.join(','); end"

   Here you provide the username, password and tns name. If this returns the current date and time then the driver is installed correctly.

6. Install DBI
   
   download the dbi tar file
   The current version is: dbi-0.1.0.tar.gz
   untar the archive
   configure it (for this example only dbi itself is included): ruby setup.rb config –with=dbi
   build: ruby setup.rb setup
   install: ruby setup.rb install
   test:

   require 'dbi'
   dbh = DBI.connect('DBI:OCI8:DEVDB.WORLD', 'username', 'password')
   dbh.select_all('select sysdate from dual') do | row |
     p row
   end
   dbh.disconnect
   

   If this returns the current date and time then DBI is installed correctly.

7. Install ActiveRecord
   
   I use gem to install active record: gem install activerecord
   
   After installing you should be able to use active record. Here is an example use:
   

   require 'rubygems'
   require 'active_record'
   
   ActiveRecord::Base.establish_connection(
       :adapter => "oci",
       :username => "username",
       :password => "password",
       :host => "DEVDB.WORLD")
   
   class TestTable < ActiveRecord::Base
     set_table_name "test_table"
     set_primary_key "some_id"
   end
   
   TestTable.find(:all).each do |tt|
     p tt
   end
   
   nac = TestTable.new()
   nac.id = 1001
   nac.some_column = "test"
   nac.save()
   
   

   One thing I learned that is someone confusing is that active record turns your primary key into a variable named “id”. So if you don’t use auto generated primary keys for some reason you can’t just assign the primary key based on the name of the column as you can any other column in the table. Instead you need to use the id field of the model.

For more information check out the following links:

• Info on oracle’s instant client
• Info on using dbi
• Info on dbi
• Info on rails with oracle

select count(1), SUBSTR(email, INSTR(email, '@', 1, 1)+1) from SOMETABLE group by SUBSTR(email, INSTR(email, '@', 1, 1)+1) order by count(1) desc

The INSTR function gives you the location in a string where another string is located. See the following link for more on the INSTR function: http://www.techonthenet.com/oracle/functions/instr.php

I’ve always found the way Oracle handles case interesting. It looks like they are changing things a little starting with 10G: http://blogs.ittoolbox.com/database/solutions/archives/005951.asp