Briknie Báez Rodríguez

Contact Info

  • e-mail: briknie.baez@upr.edu
  • GitHub: https://github.com/sbriknie

Bio:

  • French Horn player 📯
  • Computer Science Student
  • Trying to learn new things every day
  • Someday I'll like to help people with the things I do

Research Goals

By being part of the MegaProbe Lab I aim to improve my research abilities and learn a new set of skills that will help me become better scientist.

Additional Goals

  • Learn how to hack like Humberto
  • Learn how to juggle

Second Semester 2019-2020

Weekly UPDATES (LOADING, PLEASE WAIT...)

Week 8: (16-20/Mar)

  • COVID-19 IS OUT OF CONTROL!! (O.O)
  • There are rumors saying that the semester will end online...
  • We had a lab meeting through Mumble. (we just chatted with HOZ)

Week 7: (09-13/Mar)

  • Mid-Terms are Coming!
  • I didn't do much this week
  • COVID-19 is getting out of control (e.e)

Week 6: (02-06/Mar)

  • Hell week!!
  • I gave birth to a poster with the help of Luis.
  • We presented Diffhash for the first time at the SIDIM

Week 5: (24-28/Feb)

  • I installed Probably.jl at Hulk (https://github.com/jakobnissen/Probably.jl)
  • Probably.jl was downgraded from version 1.0 to version 0.1
  • We'll have to evaluate if this version suite our necessities

Week 4: (17-21/Feb)

  • I was trying to understand the code of Probably.jl to see if I can implement it to diffhash

Week 3: (10-14/Feb)

  • I helped Luis to understand how to manage real data on diffhash
  • Luis is going to run diffhash with the sea cucumber data

Week 2: (03-07/Feb)

  • This week we were working on the abstract for the SIDIM that will take place on March 6, 2020
  • We ran diffhash and started to read the code to see how we can implement the count-min sketch. Hopefully we gonna have something more solid for next week

Week 1: (27-31/Jan)

  • I had a meeting with Humberto Ortiz-Zuazaga, PhD, where we discussed the things we were going to be doing this semester.
    • I'll be retaking the diffhash project but this time I'm going to be replacing the hash function that diffhash is currently using for a bloom filter and a count-min sketch (trying to take a probabilistic aproach to see if we can make some improvements)

First Semester 2019-2020

Week 15-End: (Nov 25 - the end)

  • I am barely alive... I talked to Dr. Ortiz-Zuazaga about some problems I had with my schedule and the plan for the next semester. Hopefully I can do better next year :)

Week 14-15: (18-22/Nov)

  • Dr. Ortiz-Zuazaga tried to help us resolve the compatibility problems with the required packages but we couldn't address the problem and run the program.
  • Humberto Concluded that it was almost impossible to meet all the requirements for the preprocessing of D-GEX and we started the search for more papers on the same topic.

Week 13: (11-15/Nov)

  • Luis asked for the data to the scientist that published the paper and they answered super fast.
  • We tried to run the program from the GitHub repository of the project but we couldn't pass the preprocessing of D-GEX because of all the version issues

Week 12: (04-08/Nov)

  • Back from SACNAS... I hace like 1Kw (Kilo works, it's a standard unit of measurement hehe)
  • Humberto assigned me to work with Luis since seq-seq-pan was a an already working program with little to improve (and that little required Java)

Week 11: (28-01/Oct-Nov)

  • I went to the SACNAS Conference at Hawai'i
    • Note: Dear Mega-Probers: If you have 7 classes, do not attend to any conference... it was a bad idea :)

Week 10: (21-25/Oct)

  • Dr. Ortiz-Zuazaga Repaired Hulk!! #hulkIsBiggerThanEver.
  • I was learning how to run the code from the seq-seq-pan github but I found some problems on the way
  • Learning how to use Mauve (a tool to plot the output of seq-seq-pan)
  • Presented the Seq-Seq-Pan paper with a live demo of the Mauve tool.

Week 9: (14-18/Oct)

  • Dr. Ortiz-Zuazaga was trying to install a new graphic card into Hulk but so that we could implement a deep learning approach. However, there where compatibility problems with the old graphic and the newone.
  • #hulkWasDown
  • Lab meeting canceled, professor had a meeting.

Week 8: (07-11/Oct)

  • I was reading the seq-seq-pan paper to presented on the lab meeting.
  • Lab meeting was canceled due to BSidesPR Conference.

Week 7: (30-4/Sep-Oct)

  • Didn't have the chance to work this week.

Week 6: (23-27/Sep)

  • I went to the lab meeting to see Robertito's presentation, it was a very bad paper but Dr. Ortiz-Zuazaga got an idea out of it, so they are going to work on that

Week 5: (16-20/Sep)

  • I found a program called Mauve that look's like a good tool for the idea of the Pan-genome

Week 4: (09-13/Sep)

  • I presented the Deepfinder paper in the Journal Club
  • I'm trying to find possibles ways to create the pan-genome of the butterflies

Week 3: (02-06/Sep)

  • I started working with Steven Van Belleghem using butterfly data to create a Pan-genome
  • Lab metting cancelled

Week 2: (26-30/Aug)

  • I selected the paper "DeepFinder: An integration of feature-based and deep learning approach for DNA motif discovery." to present it at the Journal Club.

Week 1: (19-23/Aug)

  • We discussed possible ideas for projects
    • We were contemplating the use of machine learning on Papa's project

Second Semester 2018-2019

Week 8: (04-08/Mar)

  • I FINALLY PULLED!!
  • This week I am going to start reading a paper about a "better implamentation" using kmers https://doi.org/10.1371/journal.pone.0101271
  • Also I am going to work with Roberto trying to run more examples in diffhash using the polyester database.

Week 7: (25-01/Feb-Mar)

  • I was dealing with a lot of jobs from the past week and could not do many progress.

Week 6: (18-22/Feb)

  • I was studing for Abstract Algebra and Algorithms and didn't have time do anything else this week.

Week 5: (11-15/Feb)

  • Angel took the the diffhash project and he will make it work with any fastq formated file.

Week 4: (4-8/Feb)

  • I moved diffhash to Hulk because Humberto told that using R-Studio my life would be much better. Then when I started running the program and it suddently crashed and this happened:

    • Me: Professor, I think I broke something
    • Humberto: Let me see the code...
    • (10 seconds scrolling through the code)
    • Humberto: You are missing an "@." right there.
    • Everything started to run perfectly well.

Week 3: (28-01/Jan-Feb)

  • It's been a week trying to run diffhash but I haven't been able to make it run from tip to tail. I thought bioinformatics was a little bit easier 🤔

Week 2: (21-25/Jan)

  • Using the eelpondworkshop file in boqueron to run the escambron protocols in order to use real data in the program (diffhash) that our Benevolent Dictator created.
  • Trying to understant how diffhash works.

Week 1: (14-18/Jan)

  • I am trying to set some order/priorities in my life