Monday, December 10, 2012

Spanish Wine Tasting Party and Tapas

There are so many great wines out there that I have yet to explore.  I recently read Spain has one of the largest grape varieties in the world (wikipedia says over 600).  In an effort to learn about wines from another country, I decided to have a Spanish wine tasting party!  I read through many websites and it seemed the best way to expose your palette to wines from another country is to explore the range of available wines starting from the bubbly to the white wines and finally comparing multiple reds (one younger and one older).

Many spanish laws related to the classification of how long a wine must be aged have been put in place. The most common three are as follows:
Crianza:
     red - aged for at least 2 years (> 6 months in oak)
     white & rosé - aged for at least 1 years (> 6 months in oak)
Reserva:
     red - aged for at least 3 years (> 12 months in oak)
     white & rosé - aged for at least 2 years (> 6 months in oak)
Gran Reserva:
     red - aged for at least 5 years (> 18 months in oak)
     white & rosé - aged for at least 4 years (> 6 months in oak)

When I went to the store, I didn't have particular bottles of wine in mind. Instead, I asked for wines in the $10-15 range starting with a cava (Spain's version of champagne), one albariño, two riojas (one crianza, one reserva) and finally a sherry.

Wines
Here are the wines we picked and in order of tasting (from left to right):

1) Segura Viudas Aria Brut, Penedes region, Spain (blend of macabre, parellada, and xarel-lo grapes)
2) 2010 Vionta Albariño, Riax Baixas, Spain (albariño grape)
3) 2008 Cune Rioja Crianza, Rioja, Spain (tempranillo grape)
4) 2006 Cune Rioja Reserva, Rioja, Spain (tempranillo grape) - This one was the only over $15, but it was highly suggested and close enough to the budget.
5) Lustau Solera Reserva Pedro Ximenez San Emilio, Andalusia region, Spain (pedro ximenez grape)





Tapas
Since we were tasting spanish wines, we needed spanish tapas of course! :)  Here is the line up of the three tapas.

Manchego cheese (aged 1 year), chorizo, olives, crusty bread
This was by far the easiest to make. Just chop everything up and place on plate.  This was perfect to snack on at the beginning of the tasting with the cava.





Shrimp in garlic sauce (Gambas al Ajillo)
This recipe is very simple too.  I didn't follow a particular recipe because I used my mom's recipe for shrimp scampi, but just omitted the pasta.   The albariño was nice and light (good pairing with the shrimp). 

Ingredients
- 1 lb of shrimp
- 1/3 cup of fresh squeezed lemon juice
- 1/3 cup of white wine
- 1/3 cup of canola oil
- 2 garlic cloves
- handful of parsley
- salt and pepper

Recipe
1) Finely chop garlic and parsley. Mix garlic, parsley, lemon juice, white wine, canola oil and seasoning together. Set aside marinade (can be done early).


2) Clean and de-veine shrimp.  20 minutes before you are ready to cook the shrimp, let shrimp marinate in lemon garlic marinade in refrigerator.  Preheat oven to 350 degrees. 

3) After 20 minutes marinating, place shrimp and marinade in a baking dish in the oven for 5 minutes. After 5 minutes, turn on broil in oven and cook for additional 4-5 minutes.  Keep a close eye on the shrimp.   This recipe can also be used for shrimp scampi too! 




Patas Bravas
This was slightly more complicated than the first two tapas, but well worth the effort!  Bravas refers to the spicy or "fierce" tomato sauce with a bit of tabasco.  Moving along in the wine tasting, I thought the potatoes were hearty enough to pair with the riojas (red wines). 

Ingredients
- 2 lbs of baking potatoes (russet) 
- canola oil, salt, pepper
- For the sauces you can pick whatever you'd like, but I made a spicy tomato sauce and simple mayonnaise

Recipe
1) Peel potatoes and cut into 1/2'' chunks.  Place in large pot with cold water. Bring potatoes to a boil (~7-8 minutes) then immediately drain and cool potatoes under cold water to stop the cooking process. This is just to parboil the potatoes. 


2) After cooling the potatoes, pour oil in a large pan and place a single layer of potatoes in it to cook on medium to high heat. If the pan is not hot enough the potato will just absorb the oil instead of turning a nice golden brown.  Once potatoes seem brown on one side, flip them over and let them cook on another side until you have achieved the golden brown color.  After, remove potatoes to a paper towel to drain any excess oil and lightly coat with salt.  This may be need to be done in batches depending on the size of your pan.



3) Sauces. I made two sauces: a quick mayonnaise (or aioli) and a spin off of these two spicy tomato sauces (1) and (2). The tomato sauce began by sauteing 1/2 diced onion until golden and pureeing 1 can of diced tomatoes in a food processor.  Add tomatoes to onion mixture. Add apple cider vinegar, tabasco sauce, spanish paprika, sugar, salt, pepper. Bring to a boil and let simmer for 15 minutes.



We finished the tasting with the sherry (very sweet as noted on bottle).  Overall, I really enjoyed learning about the different grape varieties and their respective regions in Spain.  Hopefully it will come in handy if I ever make it to Spain someday!

Sunday, October 28, 2012

Savory Roasted Pumpkin Seeds

With fall in full swing and Halloween around the corner, we always have lots of squash and/or pumpkins around. Whether you are carving a jack-o-lantern or making a pumpkin pie, there are leftover winter pumpkin seeds which can be turned into delicious, savory roasted snacks!



Ingredients:
- pumpkin seeds (or any winter squash seeds such as my personal favorite: acorn squash)
- olive oil
- salt, pepper
- my seasoning blend: garlic powder, paprika, chipotle powder, worchestire sauce

Recipe:
1) Rinse seeds under water and remove any squash pulp. Pat dry.



2) Add olive oil.



3) Add seasoning blend. Mix well. Spread seasoned seeds on a baking sheet.



4) Bake at 350 degrees for 15 minutes. Halfway through, move seeds around so they don't stick. Let cool and enjoy!

And in case you were curious, here is our jack-o-lantern this year: pumpkin 'pi' :)



Thursday, October 18, 2012

UCSC Genome Browser: A few useful tips

Most of my research revolves around analyzing next-generation sequencing data such as whole-exome sequencing data.  As a statistician, I always appreciate finding useful bioinformatic tricks/tips from various tools that make me more efficient.  Here are three examples of using the UCSC Genome Browser that I've found helpful.

Tip #1:  How do you find a list of chromosome positions given a list of dbSNP identifiers? (Taken from the Guide to the UCSC Genome Browser FAQ by Nature)
Use the 'Variation and Repeats' group in Table Browser and the SNPs track of choice.  Just specify the genome (e.g. Human) and assembly (e.g. hg19).  For 'Region', if you want the chromosomal positions for a specific regions, click position and specify the region OR click genome and upload a list of dbSNP identifiers. Finally, choose your output format (e.g. GTF, BED) and click 'get output'.

Tip #2:  How do you lift over a set of genomic coordinates from hg18 to hg19? 
Use the Batch Coordinate Conversion (liftOver) tool in Utilities. Selected Original and New assemblies. Upload the original genomic coordinates (in a BED format) and submit.  

Tip #3: How can you extract data from the UCSC browser and use it in R? 
For this, we need to install the package rtracklayer.  Here is an example on how to extract recombination rates: 

library(rtracklayer)
my.session <- browserSession()
genome(my.session) <- "hg19"
recomb.rates <- getTable(ucscTableQuery(my.session, "recombRate"))

Tuesday, October 16, 2012

Perfect Tomatillo Salsa Verde

If you want to know how to make the perfect salsa verde with those weird green tomato-looking things with a peel (aka tomatillos), you should definitely try this recipe!  I adapted this recipe from one that looked promising:


Ingredients:
- 1-2 lbs tomatillos
- 1/2 onion
- 1 jalapeno (seeds removed unless you like a lot of heat)
- 2 cloves of garlic
- 1/4 cup of cilantro
- a pinch of cumin, paprika, salt and pepper

Recipe for Tomatillo Salsa Verde:

1) Begin with the tomatillos. Peel the skin off and rinse the tomatillos under some water.  Cut in half and place the cut-side down on a pan. Place under the broiler for 4-5 minutes until there is a nice char on the outside of the tomatillos.


2) Dump the broiled tomatillos into a food processor with onion, jalapeno, cilantro, garlic, cumin, paprika, salt and pepper.  Pulse until desired chunkiness.  I prefer mine to be fairly smooth.

Enjoy on top of some huevos rancheros, pulled pork tacosfish tacos or chips.

Tuesday, October 9, 2012

Rice University's Centennial Celebration

Rice Institute President Edgar Odell Lovett opened the Rice Institute on October 12, 1912 and this week Rice University will have its centennial celebration October 10-14, 2012! 

There are many, many events going on this week including the Centennial Lecture Series, homecoming, alumni reunion weekend, performances and parties.  I just want to highlight one of the lectures scheduled for tomorrow: 


Centennial Lecture Series #1: J. Craig Venter - Wed Oct 10 3-4pm in the Tudor Fieldhouse

AbstractPerhaps most famous for being among the first to sequence the human genome, Dr. Venter in 2010 created the first cell with a synthetic genome. He has been listed as one of the world's most influential people by both Time magazine and the British New Statesman. Venter also is tackling energy (stating that algae show promise); last year he published a high-profile paper on the first creation of synthetic life that included then-Rice student Thomas Segall-Shapiro as an author.

Calendar of all events: Centennial calendar

Google Calendar specifically for all the graduate student events: tinyurl.com/GSAcentennial

Happy Centennial Rice University!

Tuesday, October 2, 2012

Beyond the Genome 2012: Highlights and Discussion Points

This past week I attended the Beyond the Genome conference Sept 27-29 held in Boston at Harvard Medical School this year.  Genome Medicine and Genome Biology have hosted this conference for three years now and it was my first time attending.  To see more details on individual talks, check out the blogposts from Oliver Hofmann tagged with btg2012 or you can search for tweets with the hashtag #BtG2012. I want to give a few highlights from the conference, but first I'll begin with a cartoon which was a very fitting way to describe the conference!


Here are a few key discussion points I took away from the conference:
  1. Genomic or bioinformatic tools used to analyze next-generation sequencing data need to be reproducible, accessible, fast, interactive and web-based. James Taylor from Galaxy advocated for making bioinformatics more reproducible and accessible and even gave an example of in a review only 7 out of 50 papers using BWA provided all the parameters necessary to be able to reproduce their research. Gabor Marth argued bioinformatic tools shouldn't be useable by only informaticians, but also should be useable by biologists.
  2. Bioinformaticians are re-inventing the wheel. I found two recent papers giving a review of batch annotation tools for variants obtained using next-gernation sequencing (Sifrim et al. 2012; Lyon and Wang 2012) with a list of over 19 tools published just since 2010!  At the conference, several of the speakers noted in their talks, "As bioinformaticians we apparently like to keep reinventing the wheel".  I would agree with this statement.  In addition to genomic tools needing to be reproducible, accessible, fast, interactive and web-based, I would argue we need to create a standardized tool or format for annotating variants.  
  3. With mutations, context matters. Why do some of the "right mutations" not respond to treatment? Josh Stuart advocated for using pathway-based analyses to assess the impact of mutations. Should focus on recurrent, rare variants (most likely to be impactful), but also need to make sure the background mutation rate is correct and determine if mutations are in key domains such as DNA binding or conserved domains. Daniel MacArthur said we need to analyze variants in the context of tens of thousands of genomes because the human genomic landscape is dominated by ultra-rare variation and we need to require consistent variant calls across studies. He also gave a set of recommendations on establishing causality from the NHGRI (see picture below).  Lynda Chin argued even if we know the mutation changes the function of the protein, we don't necessarily know the biological consequence. Therefore she argues we need to use a model systems approach to characterize and interpret a complete catalogue of driver mutations with functional validation.  
  4. The idea of using whole exome sequencing as a diagnostic test in clinic has arrived (especially for rare genetic disorders), but we are just now starting to deal with all the challenges that come along with it.  Sharon Plon discussed her first year experience with clinical whole exome sequencing and said almost 25% of sequenced patients have "medically actionable" findings (mostly cardiac, but some cancer). Elizabeth Worthey said we need to be very careful because she explained "medically actionable" doesn't always mean "can be treated". With secondary variants and findings in clinic, Leslie Biesecker argued context matters. In his experience, the response of the patient varies depending on prior family history: with previous diagnosis - mundane response, with prior family history - mild surprise, without family history - dazed and confused.  Amy McGuire gave a beautiful talk from the legal perspective on the reasons to disclose or not disclose incidental findings and included survey results from actual GWAS researchers. In terms of drug discovery, Stuart Schreiber gave many examples of relating the genomic alterations in cancer to the small-molecule sensitivity. 

Finally, I thought the talk by Richard Gibbs deserved it's own paragraph. His talk focused on who should we be sequencing when it comes to human genetic diseases.  Though next-generation sequencing technology has come a long way, it's still not perfect.  Performing whole exome sequencing as a service can be effectively done by experts, but this is inefficient and not scalable.  Automating the process of interpretation often ends with dumb results. Sequencing healthy individuals should be a low priority especially when not tying phenotypes to the control individuals (crazy!).  Sequencing individuals with complex diseases is still tricky because of the debate regarding CDCV v. CDRV hypothesis.  He argued that if complex diseases are caused by rare variants, then we should focus within families and not broader populations.  Sequencing individuals with mendelian disease should be high on the priority list because there is a huge value in obtaining a molecular diagnosis even without a treatment.  Finally recreational sequencing is low on the priority list.  He has even coined the term 'narcciss-ome'!  Overall, he predicts sequencing will become standard of care and soon all the excitement will be passé. 

Final thoughts:  The conference was filled with fantastic talks given by world-renowned speakers.  The level of genetic complexity of diseases never ceases to amaze me, but at the same time seeing such great research being produced to answer some tough genetic questions is always exciting.  I learned a great deal and would highly recommend Beyond the Genome to future participants!  

Monday, September 17, 2012

Roasted Okra and Roasted Okra Fries

After making our gumbo, we had a bit of okra left over.  In the NFL Sunday Football spirit, I decided to try out two okra recipes: oven-roasted okra and oven-roasted okra fries. To be honest, both sounded delicious and I couldn't decide which to make, so I made both! Begin with some washed okra and patted dry with a paper towel.


Heat oven to 400 degrees.

To prepare the oven-roasted okra (pictured on left): cut the ends of the okra off and drizzle some olive oil, salt and pepper.
To prepare the oven-roasted okra fries (pictured on right): keep ends of okra on, but just slice in half, lengthwise. Do not add any oil or seasonings.


Cook in oven for 10-15 minutes, or until desired crispiness.  Remove from oven and add salt to okra fries to taste.


Results:  The oven-roasted okra fries tasted almost like fried okra, but without the calories.  They were fairly crispy and NOT soggy at all from the "slime" usually in okra.  The oven really dried out most of the moisture because they were cut in half.  The oven-roasted okra was also delicious.  It did retain some moisture, but was not too soft.  It had that oven-roasted taste (which the fries didn't) and the seeds would almost pop in your mouth.  Quite tasty!

Saturday, September 15, 2012

Shrimp and Sausage Gumbo

With football season in full swing, gumbo is very common around our household.  In fact, we like to call it our Game Day Gumbo. :) This post begins with the basic recipe, but includes a cameo appearance by Chris who explains in detail how to make the roux (most important step) in a 5 minute video.  


We've adopted a recipe from Pirate's Pantry by the Junior League of Lake Charles Louisiana.  Some of the recipes I'm not sure I'd ever dare try (e.g. Squirrel Gumbo or Turtle Soup), but it's definitely an authentic south Louisianan cookbook.  


Ingredients
For the roux: 
- 1/2 cup flour
- 1/2 cup canola oil

Everything else: 
- 1 large onion, diced
- 1/2 bell pepper, diced
- 3 celery stalks, diced
- fresh okra (or can use 1/2 teaspoon of file)
- 1 can of diced tomatoes
- seasoning blend: e.g. Old Bay Seasoning, gound cumin, ground coriander, paprika, worcestershire sauce, bay leaf, garlic, cayenne peppers, salt and pepper
- 1 lb raw shrimp
- smoked andouille sausage
- 3-4 green onions (used for garnish)


Recipe for Shrimp and Sausage Gumbo
1) Begin by prepping all the vegetables.


and gather all the seasoning you will need. In this gumbo we used Old Bay seasoning, ground cumin, ground coriander seed, paprika, worcestershire sauce, bay leaf, garlic, cayenne pepper, salt and pepper. 


2) Once everything is prepped, you are ready to begin the roux.  It really requires patience and constant stirring for a 30-45 mins (depending on fast everything goes).  Begin with the 1/2 cup flour and 1/2 cup of oil in a large dutch oven.


YouTube video: Chris created a 5 minute video to help show the process of how the roux is made.  Check out the video here.  The roux will go through different phases: tan, milk chocolate, brick and dark chocolate phase.  Here is a quick example of milk chocolate phase.


3) Once the roux is complete (again 30-45 minutes), add the vegetables and cook for 5 minutes. After, add 4 cups of water.  Stir for 2-3 minutes to help 'wash off' all the roux from the vegetables to help thicken the gumbo.


4) Add seasoning blend, diced tomatoes, diced okra, and andouille sausage (slided around 1/2 inch thick).  Add in another 4 cups of water.  Let simmer for 3 hours.


5) 20 minutes before plating, add in shrimp (or any other seafood you'd like). Stir in diced green onions right before serving over some jasmine rice.

This makes a great meal any time of the year, but highly suggested watching an exciting football game with great friends!

Monday, September 10, 2012

Perfect Herb Roasted Whole Chicken

This weekend I wanted to make a roasted whole chicken using our new roasting pan we bought this summer when we made the red snapper.  Since I've never done it myself, I wanted to make sure to follow a recipe with lots of reviewer comments.  Ina Garten has a Perfect Roast Chicken recipe that looked very promising with vegetables that roast with the chicken.  Ina puts most of her herbs inside the chicken and I was hoping to make an herb rub on the outside. So, I found an additional recipe Herb Roasted Whole Chicken which does just that.  The following recipe is my take on roasting a whole chicken.  The final product turned out incredibly moist and flavorful.  I'm looking forward to doing more roasting this fall!



Ingredients:
- 4 carrots, 2 onions, 1 fennel bulb
- sage, thyme and rosemary (or any selection of herbs)
- 1 lemon, 4 garlic cloves
- 1 whole chicken
- salt, pepper, canola oil

Recipe for Herb Roasted Whole Chicken:
1) Preheat oven to 450 degrees.  Chop carrots, 1 onion and fennel into large chunks and place in roasting pan


2) Chop sage, thyme and rosemary (~1-2 tablespoons per chicken). Add 1-2 tablespoons of canola oil and a generous handful of salt to make an herb mixture to rub on the outside of the chicken.



3) Chop 1 lemon into halves (or quarters), 1 onion into quarters, and a few garlic cloves.  Place aromatics inside the chicken and tie the legs together.


4) Lift the skin of chicken from the breast meat and place some of the herb mixture underneath the skin. Continue to rub herb mixture all over the rest of the chicken.  Salt the chicken generously.


 

5) Place chicken inside 450 degree oven for 75-90 minutes until the juices run clear and the chicken is a nice golden brown.  At this point the internal temperature is recommended to be over 165 degrees.  I let it go a little too long and it got up to 180, but it still turned out great.  


6) After you take it out of the oven, let it rest for a minimum of 10-15 minutes before slicing into it.

We paired the chicken with some herb roasted potatoes and sauteed green beans.


Friday, August 31, 2012

biomaRt: Find gene name using chromosome number and position

In a previous post, I gave a few examples of using biomaRt in R.  This is a continuation giving another useful example of using biomaRt: How to obtain gene names (e.g. HGNC) or really any information in listAttributes() function using only chromosome number and chromosome position. I was interested in obtaining the gene names for a set of mutations and decided to use biomaRt.  I created a tab-delimited file called 'positions.txt' containing three columns.  The first contained the chromosome number, followed by the start and end position (in this case they were the same).  The following code identifies what gene the chromosome position is in and reports the HGNC gene symbol.

# Load the library
library(biomaRt)

# Define biomart object
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

# Gives a list of all possible annotations; Currently there are 1668 listed
listAttributes(mart)

# Gives a list of all filters or criteria to search by; Currently there are 333 listed
# I chose to filter by: chromosome_name, start, end
listFilters(mart)

# Read in tab-delimited file with three columns: chromosome number, start position and end position
positions <- read.table("positions.txt")

# Extract HGNC gene symbol
results <- getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", "end_position"), filters = c("chromosome_name", "start", "end"), values = list(positions[,1], positions[,2], positions[,3]), mart = mart)

Wednesday, July 25, 2012

Antioxidants May Lower Risk of Pancreatic Cancer

The journal Gut (impact factor 10.11) published a prospective study yesterday investigating whether eating antioxidants such as vitamin C (found in fruits and vegetables) and E (found in nuts, seeds, egg yolk), selenium (found in cereals, nuts, fish and meat) and zinc decreases the risk of pancreatic cancer.  They looked at 7-day food diaries of 23,658 participants over 10 years in the European Prospective Investigation of Cancer (EPIC-Norfolk) Study.  The estimates in this study were adjusted for other variables such as age at recruitment, gender, smoking, diabetes, BMI and total energy (smoking and diabetes are two known risk factors for pancreatic cancer).   Interestingly, those with the highest intake of selenium, vitamin C and E reduced the risk of pancreatic cancer by two-thirds. Those with high intakes of selenium and vitamin E had 40% reduced risk.  Those are huge reductions in risk based on these micronutrients.


The American Institute for Cancer Research (AICR) wrote "37,000 Americans will die of pancreatic cancer this year. According to the National Cancer Institute, pancreatic cancer is the fourth leading cause of cancer-related death. It is often not diagnosed until the advanced stages, when treatment is challenging".  With the recent death of Sally Ride, I thought this article discussing pancreatic cancer was particularly relevant.  

Friday, July 13, 2012

War on Cancer

As a statistician applying my research to cancer genetics it is always encouraging to see stories like this that make me feel sometimes all this work isn't for nothing.

The article published last week in the NY Times describes the story of a woman who was diagnosed with a rare form of lymphoma in which white blood cells (T cells) become cancerous and move to the skin.  Faced with a disease with no cure and no standard treatment, she was able to keep the cancer at bay using chemotherapy for five years.  At that point, her health took a turn for the worse and her son who worked at Illumina, which produces some of the latest sequencing technology, decided to quit his job and help his mom full-time by sequencing her genome.  After sequencing her normal and tumor DNA, they found 18K differences (or mutations) with no known significance for disease.  In the analysis of her DNA, the researchers found two genes fused together forcing the growth signals in cancer cells to be reversed: the signal to stop was forcing the cells to grow and the signal to grow was forcing the cells to stop growth.  The researchers decided to give her a new melanoma drug ipilimumab which forces normal T cells to grow, in hopes of stopping the growth of the tumor cells. The drug performed beautifully keeping the cancerous T cells at bay for 8 weeks before the cancer came back and ultimately she passed away a few weeks later.

41 years ago Richard Nixon signed the National Cancer Act of 1971 which started a "war on cancer". The goal was to find a "cure for cancer" by increasing the funding toward cancer research and find more effective treatments.  As defined by PubMed "cancer is the uncontrolled growth of abnormal cells in the body".  Cancer is not just one disease, in fact it is the word we have for hundreds of diseases we label as 'cancer'.  When people talk about "curing cancer", it suggests that once a treatment/cure for one type of cancer is found, it should theoretically be applied to another form of cancer.  In my experience this is definitely not the case.  Every type of cancer is unique in its etiology and treatment.  It is true that some drugs today developed for one type of cancer can be applied to another type of cancer because the target molecule may happen be the same for two different cancers, but this is a separate idea than the finding a "cure for cancer".

I work with several groups of researchers in the Texas Medical Center at University of Texas MD Anderson, Baylor College of Medicine and Texas Children's Hospital who are all trying to exactly this.  They are sequencing the genomes of individuals affected by a particular disease and trying to find the causal mutation or reason for the disease.  My small contribution comes in helping to analyze the results that come out of the sequencing.  Bioinformatics attempts to take in the large amount of sequencing data and make sense of it.  This is by no means easy and will take much longer to properly analyze the data than to just sequence it.  But, even with these small steps I look forward to more success stories like these and seeing further progress being made in the war on cancer.

Tuesday, July 10, 2012

Making a movie out of images .png using ffmpeg

Say you are interested in plotting in three dimensions in R.  This can be quickly done using the rgl package in R.  There are functions called plot3d(), persp3d() and lines3d() which let you plot in three dimensions, light3d() which adds a light to the background, bbox3d() which edits the colors of the 3d box, and view3d() which picks the particular angle of view.  One idea is to quickly write a for loop within R to rotate the image 360 degrees to get a nice little rotation of your 3d image.

Now, say you are interested converting the 360 different views in R into 360 images with a .png format.  This can be done within the rgl package using the rgl.snapshot() function.  In R, type the following

# Load rgl library
install.packages("rgl")
library(rgl) 


# Plot 3d image
plot3d(x, y, z)

# For loop rotating the 3d image 360 degrees
degrees <- seq(1,360, by = 1) # a sequence from 1 to 360
for(i in 1:length(deg)){
    view3d(degrees[i], phi = 0) # pick the angle of view
    rgl.snapshot(paste(paste("/file_directory/filename", "-", 
        formatC(i, digits = 3, flag = "0"), sep = ""), "png", sep = "."))
}

formatC() is a function that will add -001, -002, -003 etc to each of your images. This will be important in a moment.  

Finally, say you are interested in converting these 360 images to a movie.  I came across a great blogpost that showed me the commands to quickly and painlessly accomplish this.   It requires the use of the ffmpeg command in the terminal. In the terminal, type the following: 

$ cd ./location_of_file/file_directory
$ ffmpeg -f image2 -i filename-0%3d.png video.mpg

This converts the 360 images named 'filename-0001.png', 'filename-0002.png' etc to a video named video.mpg.  I know this won't make sense to most people, but here is what I ended up with: 

video


Tuesday, July 3, 2012

Dark Chocolate Mousse

Recently, I attempted my first chocolate mousse recipe from scratch.  I must admit, it was easier than I thought it was going to be.  I looked around for several recipes including one that replaced the cream and eggs with avocado, but I decided for my first mousse I would keep it classic.


I decided to follow Bobby Flay's recipe which only had four ingredients in it: 6oz dark chocolate, 14oz heavy cream, three egg whites and 1oz sugar.  The recipe was very straight forward.  Start with some high quality chocolate (preferably > 70% cacao):


To melt the chocolate, Bobby suggests using a double boiler, but Ina Garten said on Barefoot Contessa that you can always just put chocolate in the microwave for 20 seconds, take it out, stir, put back in microwave for 20 seconds and repeat.  When it is almost melted (but still has a few chunks) just take it out, stir and the rest of the chocolate will melt naturally (to avoid burning it).  Next, whip the cream until stiff peaks and set aside.


Third, whip the egg whites and slowly add in sugar until stiff peaks. Mix the melted chocolate with the egg whites all at once.  Once everything is mixed, start to slowly fold in the whipped cream into the chocolate mixture.  Separate mixture into four ramekins (or wine glasses) and place in fridge to set up for at least 1 hour.  When ready to serve, top with a few pieces of fruit and some coco powder. Hopefully you will enjoy it as much as I did!  This will definitely be a repeat dessert.



Monday, July 2, 2012

Cooking Whole Red Snapper

The last few weeks have been very busy with research and a bit of traveling.  Lots of changes are happening with me and Chris, but one thing has definitely not changed: our culinary interest in learning about new foods and new recipes.  This weekend we set out on an adventure to learn how to cook an entire fish (yes, head and all).  After watching several videos and reading many, many recipes, we decided to follow Alton Brown's recipe.  He uses striped bass, but we knew we were just going to pick whatever was fresh at Central Market.

To begin, we realized we were going to need a roasting pan of sorts.  The closest thing we had was a flat sheet pan or a small clear 8x8 pyrex pan.  In last minute trip to Bed Bath and Beyond, we picked up a very nice Calphalon Tri Ply 14'' Roaster.


Interestingly it came with a rack and lifters which will be perfect for roasting chickens or our first turkey this fall. :)


Now that the pan had been secured, we set off to Central Market to buy a fish. As a side note, we had also heard that in Houston another great place to buy fresh fish was J & J's Fish Market.  Next time we will probably check that out.  For now, back to Central Market.  The guy behind the fish counter (I believe David was his name) was so nice when we told him we wanted to buy two whole red snappers.  


He offered to de-scale, de-fin and clean up the snapper for us even though it took him a full 5-10 minutes (on a Saturday afternoon in Central Market with a line of people behind you, that was incredibly generous of him for taking the time to do that for us).  


After putting it on ice and getting the fish safely home, we started to chop of the aromatics needed for recipe.  You begin by making a bed of parsley and dill.


Add some sliced onion and lemon to the party.


Add fish on top of the aromatics.


Add more parsley and dill on top of the fish.


Cover with aluminum foil and place in a 500 degree oven for 35 minutes or until an internal temp of 120 degrees.


We served it on a bed of fresh parsley with some lemon.



It turned out to be delicious!  The only troubling thing was the bones.  Not sure if there is a polite way to spit out a bone? :)  Either way, I would definitely recommend this recipe to anyone interested in learning how to cook a whole fish.  We also had a lot of fun along the way.