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Computer Scientist at the Department of BioSciences, Rice University

Archive for September, 2013

Installing and setting up KINSOLVER in a Linux 2.6.32-358.6.2.el6.x86_64

September 29th, 2013 by Boanerges Aleman-Meza

Steps that I followed to install KINSOLVER in a linux-box 2.6.32-358.6.2.el6.x86_64

  1. Get the KINSOLVER C++ source code
    1. Created folder ~/kin_c_source
    2. Downloaded Makefile, kin.cpp, kin.h
    3. Compiled executable via command-line: make
    4. Make folder ~/kin
    5. Copy executable kin_c to ~/kin/
    6. The backend simulator (executable) is then located at ~/kin/kin_c
  2. Get the Java KINSOLVER source code
    1. Created folder kin_java_source
    2. Downloaded Java files (Dataset.java, KinFile.java, …, and )
    3. Update PlotServlet.java to make sure that the URL is updated accordingly (e.g., change from genetics.uga.edu to your own server)
    4. Update the script to compile (compile.sh)
      1. The jar file for servlets may need to be specifies, such as using the one in apache tomcat. Example: /opt/apache-tomcat-7.0.40/lib/servlet-api.jar
  3. Make sure Gnuplot works
    1. For example, admin had it installed at: /usr/bin/gnuplot
  4. Setup java-servlets
    1. Inside folder ‘jsdk2.1’, update variables inside of file: kin_environment.properties
    2. Start the servlet-server by running ./startserver
      1. Verify that the servlets are running by going to http://odyssey.bioinformatics.uga.edu:8090/kin/servlet/Setup , which is a servlet that keeps track of the options needed to  run KINSOLVER
      2. In the case that the browser takes a while to show anything and times out, then likely the port (i.e., 8090) is not accessible either in the network (such as inside campus computers) or the linux-box has the port closed (system-administrator needs to open the port)
    3. Go to servlet with configuration options, save changes, and click on “create web page”
  5. Test via uploading an input file
  6. Troubleshoot until it works
    1. For example, I changed ‘kinnew’ to ‘kin’ in order to have simpler URLs
    2. Reminder: changes on java-servlets code requires stopping the server and starting it up again to be visible
      1. Inside folder ~/jsdk2.1
      2. Start server: ./startserver &
      3. Stop server: ./stopserver
        1. In case of error messages when stopping it, just ignore them.

The genius in All of Us

September 7th, 2013 by Boanerges Aleman-Meza

Excerpt of Moira Gunn’s interviewing David Shank on his book The Genius in All of Us:

DAVID: This is all about how to fail. Growing up is all about failing and learning from the failure and developing a good attitude about that. If we tell kids that they are just really good at stuff because they’re born that way, that is a disaster emotionally because they are like “oh. I’m good. I don’t don’t wanna try stuff that feels bad or difficult because I’m just good this stuff and I just stick in that, you know, I’ll just stick in that area”.

MOIRA: You were talking about parenting earlier. One thing that you talk about that I think is really important is, don’t attach love or affection to achievement. [emphasis added]

DAVID: Yeah, this is a, uh, it actually turns out to be a quite a good recipe for creating prodigies, if that’s what you want. You know, if you want someone, what you do is, you get the short term pay off of kids earning that love and affection through this incredible hard work of becoming good at something. And  then they turn into adults, and they don’t know what love is, and they don’t know what human relationships are, because they’ve been taught about this transaction, which is very, it is very harmful.

Link to MP3 file of the interview.

Recipe for charro-beans (blend americanized version)

September 5th, 2013 by Boanerges Aleman-Meza

Recipe for cooking charro beans, aka, frijoles charros or frijoles rancheros, somewhat blend (americanized), adapted from existing recipe for frijoles charros.


  • 2 lb. beans (normally I use pinto beans)
  • 1/2 lb. bacon
  • 1/2 lb. ham
  • 4 tomatoes + 4 green tomatoes (or their equivalent to the 4 red tomatoes)
  • 3 garlic cloves
  • 1 tbsp salt
  • 2 onions
  • 1 chicken boullion (sounds like a bully but it is not)
  • cilantro (normally I use 1/3 of the chunk, or about 20 stems)
  • Pork skins (one bag of normal size of snack would do)


  1. Clean the beans to avoid stones (you’ll hate a stone, your dentist may like it)
  2. Clean all the veggies
  3. Add lots of water into a pressure pot, add the beans, 1 tbsp salt, 1 garlic clove, 1 onion, then when boiling, adjust flame to avoid exploding the pressure pot, and cook for 35 minutes
  4. Fry the tomatoes and green tomatoes, and the remaining garlic cloves (cut them along the long side in 2 or 3 parts), then use a blender to blend them together with the cilantro and the chicken bouillon
  5. Chop the onion in small parts (approximately the size of squares of 4 millimeters by 4 millimeters)
  6. Fry the bacon until it starts to get golden color, add the onion and fry until the onion is transparent, add the ham and cook for 5 minutes at medium flame or so
    • The original recipe would include chorizo here but some people think it is too strong flavor
  7. When the pressure pot is done with the beans, trash the onion and the garlic clove
  8. Add the stuff you blended into the pressure pot
  9. Add the stuff you fried (bacon, onion, ham) into the pressure pot
  10. Add the pork skins into the pressure pot
  11. Wait until it starts boiling (with no lid) and then cook it for 5 minutes

Mexican beef caldo recipe (soup of beef and veggies)

September 4th, 2013 by Boanerges Aleman-Meza

Recipe to make beef caldo (caldo de res), adapted from an existing caldo de res recipe.


  • 1 tbsp salt
  • 1 clove of garlic
  • 1 onion
  • 3 lbs. beef shanks center cut bone-in
    • I never find it in Kroger, always found it at HEB
    • Alternative: Short Loin with bone
  • 1 lb. butter gold potatoes (or is it honey gold?)
    • I normally use 3 lb. bag because it is a better deal buying the bag
    • I cook them as indicated in the procedure, but when done, I separate them in a different container to avoid having a plate that has too many potatoes in it
  • 1 lb. carrots
    • If you’re rich or want to save time, buy the baby-size carrots
  • 3 corn in the cob
  • cilantro (normally I use 1/3 of the cilantro, or about 20 stems)
  • 5 squash (a.k.a., calabacitas)


  1. Clean all vegies
  2. Use a pressure pot to cook the beef, together with lots of water, the onion, one clove of garlic, and 1 tbsp salt.
    • When boiling, change the flame accordingly so that the pressure pot does not explode and cook for 30 minutes
  3. Depending on the size of the pressure pot, remove (or not) the beef
  4. Trash the onion and the garlic
  5. Peal the potatoes and cut them in half, cut each squash in four parts, cut the carrots in spoon-size chunks
  6. Add everything else into the pressure pot
  7. When boiling, adjust the flame and cook for 1 minute
  8. All done!