Archive for April, 2008

How to install Open Source Ecommerce Magento Software and PHP 5.2 on CentOS 5 Linux

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Magento is a new, feature-rich open source ecommerce software, it is much better than ecommerce software developed with PHP such as OSCommerce, Zen Cart, X-Cart, CubeCart etc. I believe someday it will be another Zimbra.

To install Magento on CentOS 5, you need to install PHP 5.2, which is not available for current CentOS version.

1, Add Jason Litka’s yum repository to your yum repository.

rpm –import http://www.jasonlitka.com/media/RPM-GPG-KEY-jlitka

yum utterramblings http://www.jasonlitka.com/media/EL5/i386/

vi /etc/yum.repos.d/utterramblings.repo :

[utterramblings]
name=Jason’s Utter Ramblings Repo
baseurl=http://www.jasonlitka.com/media/EL5/i386/
enabled=1
gpgcheck=1
gpgkey=http://www.jasonlitka.com/media/RPM-GPG-KEY-jlitka

yum update

2, Install php-mcrypt

yum install php-mcrypt

3, Restart Apache

apachectl restart

4, Fix Zen Cart if you are running an old version of the software and you see these errors in the error log file:

PHP Fatal error: Call to a member function Execute() on a non-object in /xxx/xxx/zcart/includes/functions/sessions.php on line 61

edit /xx/xxx/zcart/includes/functions/sessions.php, change

    function _sess_write($key, $val) {
      global $db;
      global $SESS_LIFE;

to

   function _sess_write($key, $val) {
      // The following is only to work around a PHP 5.2.0 bug:
      global $db;
      if (!is_object($db)) {
        //PHP 5.2.0 bug workaround ...
        $db = new queryFactory();
        $db->connect(DB_SERVER, DB_SERVER_USERNAME, DB_SERVER_PASSWORD, DB_DATABASE, USE_PCONNECT, false);
      }

      global $SESS_LIFE;

5, Install APC (Alternative PHP Cache) cache

yum install php-pear

yum install php-devel httpd-devel

yum groupinstall ‘Development Tools’

yum groupinstall ‘Development Libraries’

pecl install apc

press enter when

the install stop at this line:

1-1, ‘all’, ‘abort’, or Enter to continue:

create a file /etc/php.d/apc.ini with the following lines

extension=apc.so
apc.enabled=1
apc.shm_size=30

restart apache

/etc/init.d/httpd restart

6, Create a phpinfo.php file and check if Apc is enabled

<?php phpinfo(); ?>

7, Now you are ready to install Magento

8, If your WordPress is not working after installing apc, you may want to remove apc.ini from /etc/php.d/.

9, If you see the following error in apache error log:

[warn] RewriteCond: NoCase option for non-regex pattern ‘-f’ is not supported and will be ignored

You should change the following line in your .htaccess or httpd.conf

RewriteCond %{REQUEST_FILENAME} !-f [NC]

to

RewriteCond %{REQUEST_FILENAME} !-f

or remove the entire line

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GR Safe Nucleic Acid Stain, An Excellent Alternative to Ethidium Bromide, Safety, Sensitivity, Stability

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GR Safe can:

  • Save money for your lab
  • Avoid DNA mutation caused by ethidium bromide and UV light.
  • Offer a safer and better alternative to ethidium bromide and expensive SYBR brand stains
  • Eliminate risks to yourself, the environment and your institution

Feedbacks from Customers:

  • Thanks for the free sample, it works and we are buying more.
  • Good for my teaching class (high school).
  • Nice stain.
  • Better than EB!

Description: GR Safe is a new, safe nucleic acid stain for detecting double-stranded DNA, single-stranded DNA, and RNA in agarose gel. It can be used for replacing mutagenic ethidium bromide (EB). GR Safe emits green fluorescence when bound to dsDNA and red fluorescence when bound to ssDNA or RNA. This new stain has two fluorescence excitation maxima when bound to nucleic acid, one centered at approximately 290 nm and one at approximately 490nm. GR Safe is as sensitive as EB, and much cheaper than SYBR Green, SYBR Gold and SYBR Safe, and you can use GR Safe just as the way you used EB.

Compared to EB which is a very strong mutagen, GR Safe caused very few mutations in the Ames test. In addition, GR Safe had a negative result in mouse marrow chromophilous erythrocyte micronucleus test and mouse spermary spermatocyte chromosomal aberration test.

  • Available at 10,000X in H2O for better safety –No more toxic and flammable organic solvent
  • Room temperature storage for better convenience, stable at room temperature for years –No more freeze-and-thaw cycle!
  • As sensitive as Ethidium Bromide and SYBR Safe –With confidence in your mind: it works! .
  • Add GR Safe to warm agarose gel solution as you did with ethidium bromide before–No need to do lengthy post electrophoresis staining, save your valuable time.
  • DNA bands can be viewed using either UV or safer Blue Light Transilluminator. If you use Blue Light transilluminator, you will not expose to dangerous UV light, so you will not get sun burn or skin cancer or damaged eyes.
  • You can use digital camera to take gel photos: No need to use expensive gel documentation equipment or Polaroid Camera and films.
  • Will not affect downstream experiments: compatible with all gel purification kits tested, will not inhibit ligation reaction etc.
  • Compatible with Sodium Borate Electrophoresis Buffer: Run gel 2-3 times faster at higher voltage, resolve shaper bands in minutes, and less heat generation.
  • Watch DNA migrate at your bench, in real-time without UV light (LED bluelight lamp is available from http://www.labsupplymall.com.)
  • Cut out DNA bands for subclonning under safer blue light: No mutations caused by EB and UV light. (Blue Light transilluminator will be available from http://www.labsupplymall.com soon).

Sensitivity:

p>GR Safe vs EtBr

GR Safe EtBr

Storage: Store at room temperature.

Disposal:

  • Gel: Biosafety trash bag.
  • TAE or Borate Buffer Solution: sink or consult a chemical safety officer at your institution.

Protocol:

1. Prepare 40 ml of agarose gel solution (concentration from 0.8~2.0%) with TAE or Borate Buffer in a 250 ml flask and mix it thoroughly. Place the flask in the microware, heat on high until the solution is completely clear and no small floating particles are visible (about 2~3 minutes).

2. After the gel solution cool to about 55 oC, add 2 µl of GR Safe to the solution. Swirl the flask gently to mix the solution and avoid forming bubbles.

3. Pour the gel solution into a gel tray until the comb teeth are immersed about 1/4~1/2 into the gel solution.

4. After the agarose gel has solidified you can perform electrophoresis using either 1X TAE or 1X Borate Buffer (Available from http://www.labsupplymall.com).

5. Detect the bands using UV or blue light transilluminator.

FAQ

1, What filter should I use for blue light transilluminator?

Amber filter. You can buy it from www.bhphotovideo.com, www.adorama.com, www.ritzcamera.com or www.wolfcamera.com

2, Where to buy blue light transilluminator?

www.invitrogen.com/safeimager, www.clarechemical.com/transilluminator.htm.

3, Where to buy blue light LED (torch) for monitoring gel and cutting DNA band from gel?

Ebay, Ebay Motors or other on-line stores

4, I got high background, what should I do?

Use less GR Safe, e.g., 1 ul/per 100 ml gel solution

5, Can I use UV transilluminator?

Yes. You can also convert UV transilluminator to Blue light transilluminator using a UVP VISIBLUE CONVRTR PLATE, 21X26 cm. This item can be purchased from VWR (Cat# 15000-088, $318.00).
Visi-Blue Converter Plate. 21Wx26Lcm. Designed to convert UV light to 480nm blue light for use with GR Safe, SYBR Green, SYPRO Orange and EGFP stains. Scratch resistant blue Plexiglas surface is safety fused into metal frame for durability. For UVP transilluminators.

6, Is is safer than SYBR Safe?

Yes or equivalent, but better and cheaper.

7, Is it more sensitive than SYBR Safe?

Yes or equivalent, but better and cheaper.

Other Related Items

1, New unused Qiagen QIAprep Spin Plasmid Miniprep Kit, 250 spin columns For 250 purifications of up to 20 ug molecular biology grade plasmid DNA.

2, New Qiagen EndoFree Plasmid Maxi Kit (10), Cat # 12362 containing 10 QIAGEN-tip 500, Reagents, 10 QIAfilter Maxi Cartridges, Endotoxin-free Buffers.

3, New QIAGEN Plasmid Maxi Kit (10), Cat # 12162, containing 10 QIAGEN-tip 500, Reagents, Buffers.

4, New Qiagen RNeasy Mini Kit (50), Cat # 74104, containing 50 RNeasy Mini Spin Columns, Collection Tubes (1.5 ml and 2 ml), RNase-free Reagents and Buffers.

5, New unopened Invitrogen Lipofectamine 2000, Cat # 11668-019, 1.5 ml,

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WordPress Social Bookmarks Plugins: “Share This” vs “Social Bookmarks”

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After installing Alex King’s “Share This” plugin I found my blog site was super slow. I checked the code and found out the problem is the javascript used by “Share This” plugin was not installed locally –it was downloaded from http://sharethis.com every time the page was viewed. In another word, your web site will be slow if sharethis.com is slow.

So you should uninstall Alex King’s stuff and install Social Bookmarks Plugin for WordPress from http://www.dountsis.com/projects/social-bookmarks.

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