Commit 2399d22c authored by Ricardo Avila's avatar Ricardo Avila
Browse files

Merge branch 'projects' into landing_page

parents e934c9c7 b150c82f
......@@ -10,8 +10,8 @@ timezone: America/Denver
# Author and Social
author:
name: Ricardo Avila
avatar: # path or url of avatar image (square)
bio: Ricardo Avila is a data scientist and structural bioinformatician.
avatar: /assets/author.jpg # path or url of avatar image (square)
bio: Ricardo Avila is a bioinformatics nerd, artist, and lover of open source software.
email: ravila@protonmail.com
linkedin: ravila4
github: ravila4
......@@ -165,6 +165,7 @@ defaults:
nav: notes-nav
aside:
toc: true
show_date: false
## posts
- scope:
path: ""
......
Ricardo Avila:
name: Ricardo Avila
avatar: assets/author.jpg
bio: Ricardo Avila is a bioinformatics nerd, artist, and lover of open source software.
email: ravila@protonmail.com
linkedin: ravila4
githib: ravila4
gitlab: ravila4
Yuejiao Xian:
name: Yuejiao Xian
avatar:
bio:
email: xianyuejiao@gmail.com
linkedin:
github:
......@@ -15,40 +15,40 @@ header:
url: /cv.html
- title: <i class="fas fa-bookmark"></i>
url: /notes/notebook.html
url: /links.html
notes-nav:
- title: <i class="fas fa-flask"></i> Bioinformatics
children:
- title: E-values and bitscores
url: /notes/bioinformatics/e-value-bitscore
url: /notes/bioinformatics/e-value-bitscore.html
- title: <i class="fas fa-database"></i> Databases
children:
- title: SQLite
url: /notes/database/sqlite
url: /notes/database/sqlite.html
- title: <i class="fab fa-python"></i> Python
children:
- title: Anaconda
url: /notes/python/anaconda
url: /notes/python/anaconda.html
- title: Dash
url: /notes/python/dash
url: /notes/python/dash.html
- title: Pandas
url: /notes/python/pandas
url: /notes/python/pandas.html
- title: <i class="fas fa-laptop"></i> UNIX Stuff
children:
- title: Docker
url: /notes/unix/docker
url: /notes/unix/docker.html
- title: Flatpak
url: /notes/unix/flatpak
url: /notes/unix/flatpak.html
- title: Git
url: /notes/unix/git
url: /notes/unix/git.html
- title: jq
url: /notes/unix/jq
url: /notes/unix/jq.html
- title: Miscellaneous Utilities
url: /notes/unix/misc-utilities
url: /notes/unix/misc-utilities.html
- title: One-liners
url: /notes/unix/one-liners
url: /notes/unix/one-liners.html
- title: Regular Expressions
url: /notes/unix/regex
url: /notes/unix/regex.html
- title: Systemd
url: /notes/unix/systemd
url: /notes/unix/systemd.html
---
layout: notes
title: Ricardo's Notebook
aside:
toc: true
sidebar:
nav: notes-nav
show_date: false
---
This is where I write notes on various topics.
```
.--. .---.
.---|__| |~~~|
.--|===|--|_ |~~~|--.
| |===| |'\ .---.--| |--|
|%%| U | |.'\ |===|%%| | |
|%%| N | |\.'\ | | | | |
| | I | | \ \ |===| | | |
| | X |__| \.'\ | | |~~~|__|
| |===|--| \.'\|===|%%|~~~|--|
^--^---'--^ `-'`---^--^---'--'
```
......@@ -7,10 +7,9 @@ sidebar:
nav: notes-nav
---
- [Branch](#branch)
- [Stash](#stash)
- [Branching](#branching)
## Branch
## Branching
Deleting a local branch:
......@@ -18,7 +17,23 @@ Deleting a local branch:
git branch -d branch_name
```
## Stash
Deleting a remote branch:
```
push --delete remote_name branch
```
Checkout specific files from another branch:
```
git checkout branch_name file file2
```
Merge a specific commit to current branch:
```
git cherry-pick 63344f2
```
Hide branch changes:
......@@ -30,4 +45,4 @@ Restore branch changes:
```
git stash apply
```
\ No newline at end of file
```
---
layout: notes
title: Miscellaneous Unix Utilities
title: Miscellaneous UNIX Utilities
aside:
toc: true
sidebar:
......
......@@ -59,7 +59,7 @@ uniprot_to_pdb.head()
<figcaption>A sample of the SIFTS Data Frame.</figcaption>
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......
......@@ -133,7 +133,7 @@ cmpd_activity.head(3)
`(382291, 7)`
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......@@ -215,7 +215,7 @@ protein.head(3)
`(20244, 6)`
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......@@ -295,7 +295,7 @@ target.head(3)
`(2211, 5)`
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......@@ -459,7 +459,7 @@ result.head(3)
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......
......@@ -80,7 +80,7 @@ data_logp.head()
`Shape: (707, 7)`
<div style="overflow-x: scroll;">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......@@ -228,7 +228,7 @@ X.head()
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......@@ -460,7 +460,8 @@ for f in fps:
scores[f] = {}
# Convert fps to 2D numpy array
X = np.array(fps[f].tolist())
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33, random_state=42)
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33,
random_state=42)
for m in models:
models[m].fit(X_train, y_train)
#scores[f][m + "_r2_train"] = models[m].score(X_train, y_train)
......@@ -479,7 +480,7 @@ scores_df
<div style="overflow-x: scroll">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
......
......@@ -27,7 +27,7 @@ Thus, I have access to a very convenient and ever-growing virtual library of boo
Enter here AbeBooks.com. Next to Amazon, and occasionally Ebay, it is my go-to site for buying cheap used textbooks.
Given that I have stored the ISBN data for most of my electronic books, I would like to be able to automatically fetch pricing information for any book in my virtual library, perhaps even keeping track of changes in price over time.
However, until now, the main problem stopping me from writing a script to do this, was that AbeBooks does not have a publicly available API... or at the very least, none that is explicitly documented.
However, until now, the main problem stopping me from writing a script to do this was that AbeBooks does not have a publicly available API... or at the very least, none that is explicitly documented.
![](/assets/images/abebooks/abebooks.png)
......
.author-profile {
align-items: center;
max-width: 25rem;
padding: map-get($spacers, 2) map-get($spacers, 3);
margin: map-get($spacers, 4) 0;
......@@ -9,10 +10,11 @@
}
}
.author-profile__avatar {
width: 5rem;
height: 5rem;
width: 6rem;
height: 6rem;
margin-top: map-get($spacers, 2);
border-radius: 50%;
margin-right: map-get($spacers, 2);
border-radius: 10%;
}
.author-profile__name {
font-size: map-get($base, font-size-lg);
......
......@@ -26,7 +26,7 @@ titles:
key: page-about
---
Hi! My name is Ricardo Avila. I enjoy researching computational problems in biology, ranging from protein structures, to genomic sequences and chemical structures. I find that the most difficult and rewarding problems often require connecting seemingly unrelated fields. Hence, I enjoy being in the overlap of different disciplines, figuring out how things come together.
Hi! 👋 My name is Ricardo Avila. I enjoy researching computational problems in biology, ranging from protein structures, to genomic sequences and chemical structures. I find that the most difficult and rewarding problems often require connecting seemingly unrelated fields. Hence, I enjoy being in the overlap of different disciplines, figuring out how things come together.
I grew up in the sunny city of El Paso, Texas, and graduated from the University of Texas at El Paso (UTEP), where I studied a Bachelor's of Science in Biochemistry, and a Master's degree in Bioinformatics. My current research involves machine learning methods for drug discovery, but I'm also very interested in protein structure and molecular simulation.
......@@ -35,7 +35,7 @@ In my free time I like drawing, taking photographs, reading science fiction, and
## About this site
This blog has seen several iterations in my attempt at finding the best format for writing. I needed something that can easily display code, documentation and mathematical formulas. Therefore, I have settled on writing these posts in markdown using Jekyll, and hosting the source code on GitLab.
This blog has seen several iterations in my attempts at finding the best format for writing. I needed something that can easily display code, documentation and mathematical formulas. Therefore, I have settled on writing these posts in markdown using Jekyll, and hosting the source code on GitLab.
In this small blog, I plan to make regular posts about bioinformatics projects, and miscellaneous code snippets. Most of the time I am coding in Python, R, or BASH... but I will post about whatever I am learning at the moment. My main motivation is that I frequently find myself trying to remember the solution to an old problem that I know I solved before, but spending a long time trying to remember which project it came up in. Hence, I have decided that blogging would be a good habit to build. I am hoping that some of these posts can be helpful to other people as well.
......@@ -44,8 +44,7 @@ In this small blog, I plan to make regular posts about bioinformatics projects,
I'm friendly! If you have any questions or comments, feel free to shoot me an email.
__Email:__ ravila@protonmail.com
📧 ravila@protonmail.com
<div class="card">
<div class="card__image">
......
---
layout: article
title: Links
show_date: false
---
## [Ricardo's Notes](/notes/bioinformatics/e-value-bitscore)
Notes on various topics.
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