Summary:  Email in the organization goes down, but students not affected because they use google-email. We should also have google email, oh wait, nevermind.

“Undergraduate email did not appear to be affected by the hardware failure” was the message in IT describing the email issues in campus yesterday.

The organization I work for uses one of those Webmail services installed by IT to provide email to staff. Students, on the other hand, are given email services through Google. I’m not aware of how much Google gets paid for this but that does not matter.

When email goes down, people are not happy. Even if it went down for only a few hours. So, what are the options?

• We all should be moved to email service by Google. This option has the drawback that if the service fails, absolutely no one in the organization would have email.
• We should use some other email service but I am not fully satisfied with Yahoo’s web client, neither Outlook’s design.
• Strengthen IT’s capacity to deal with hardware failures. I like this option because as much as I like google-email, I like it more that my organization is independent on something so important as email.

Somehow this issue brought up another topic, online storage. It turns out that some people in the organization prefer to use Dropbox instead of the in-house solution because it costs less and it is easier to use (I don’t have data to back this up myself, no pun intended).

How could this be possible? I’m no IT system support guy (thanks God) but I know that 2TB disks are below $100USD and a server with space for 8 disks costs less than $1,000 for sure.

Is it necessary for an IT department (or Cloud department, whatever) to actually make money out of their in-house options? (that’s how it looks like). I know they have running costs, but I thought such departments are a service for the organization. It is not like the Parking folks, who can only build a parking deck with millions of dollars investment up front.

On a final note, some one told me that the off-campus data center is in a reconditioned “house” that used to be thought to be full of spirits and ghosts. Such ghosts now guard our data off campus. Happy late Halloween then!

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.

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

Ingredients:

• 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)

Procedure:

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

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

Ingredients:

• 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)

Procedure:

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!

Here are a few of my notes about genetics.

Mendelism: Mendel is second on my list of top scientists, just right after Darwin.

Vocabulary:

• Gametes: they usually have only one copy of each chromosome (such as sex cells)
• Zygote: single cell from female gametes and male gametes. “I’ve been using internet before you were a zygote” said Dave Winer, I think.
• Monohybrid cross: a single trait is studied
• Dihybrid cross: two traits are studied.
• Haploid eukaryotic cells have one copy of each chromosome.
• Diploid eukaryotic cells have two copies of each chromosome.

Worth remembering:

• In substrate pathways, double mutant shows the upstream gene
• In signaling pathways, double mutant shows the downstream gene
• if A suppresses B and A is loss-of-function, then there will be too much B
• mitosis: duplication into sister chromatids, everything is lined-up in the middle.
• meiosis I: we have 2 cells, separate homologs, homologs are lined up
• meiosis II sister chromatids separate
• recombination: if 100% of tetrads have a crossover, the % of number of progeny showing recombinant types is 50

These are (some of) my favorite places to eat in Houston Texas. (In no particular order)

• Blue Nile Ethiopian Restaurant, 9400 Richmond Ave
• Skip this when having people that only like americanized food
• Hibachi Grill and Buffet, 12183 Katy Freeway
• Toddler friendly menu (which buffet is not toddler friendly?)
• It has changing station only on women’s restroom
• Nam Noodles and More, 2512 Rice Blvd
• Toddler should be able to eat noodles or tofu, and the chocolate cake for sure
• Some tables have a long sofa-like on one side, which is good for toddler to jump around
• It has changing station in both men’s and women’s restroom
• Torchy’s Tacos, 2400 Times Blvd
• Toddler friendly menu, we like the dirty-chavez because of the egg although the carrots need to be eaten by adult (they are spicy)
• It has changing station in both men’s and women’s restroom
• Tofu Village, 9889 Bellaire Blvd #303
• Toddler can eat rice, tofu (choose either not spicy or mild), pancake
• It does not changing station in any restroom

Adapted from an existing recipe for Mexican green salsa

Ingredients:

• 1 onion
• 1 clove of garlic
• 4 tomatoes
• 2 serrano pepers
• 20 sticks of cilantro
• salt

Procedure:

1. Wash everything
2. Put a small chunk of onion (approx. 1/8th of the onion), the tomatoes, serrano pepers and the garlic on a frying pan on high flame until they burn a little. For example, the tomato should be cooked enough so that its skin could be easily removed by hand
3. Blend everything (except the tomatoes), adding 1/4 cup of water and 1/2 tsp of salt
4. Add the tomatoes to the blender and blend again but only enough so that the tomatoes are sort of chopped instead of fully blended.

When my daughter was a baby, my wife and I would sing to her to help her in falling sleep.

These are the spanish songs that I liked to sing to my daughter.

• Amor eterno – Rocio Durcal
• Siempre en mi mente – Juan Gabriel
• Duérmete mi niña duérmeteme ya porque viene el coco y te cantará
• 100 años – Pedro Infante
• Destino – Ana Gabriel
• A la camita – Topo Gigio