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Lemas Lab

This is the repository for the Lemas Lab Group. We use Jekyll to run our Github page. Feel free to fork and make your own page or submit a pull-request!

Procedure to make change

  1. Login your Github account.
  2. If you are using Windows and have never installed or used Git, please go to this website to install Git first. Otherwise, skip this step.
  3. Open command line, direct to the folder in which you want to save the source code of the website.
  4. Clone repository to your local machine with the following command line:
git clone https://github.com/lemaslab/lemaslab.github.io.git
  1. Change directories to the cloned repository.
cd lemaslab.github.io
  1. Create your own branch. Skip this step if you already have your own branch.
git branch <create-branch>
  1. Switch to the appropriate branch you are working on.
git checkout <branch-name>
  1. Make appropriate changes to the cloned repository to update information to the webpage.
  2. Test if the updated repository can run appropriately on your local machine following the procedure: Requirements -> Step2 -> Step4 on this guideline.
  3. Type the following lines to update the repository:
git add -A
git commit -m '{describe your change}'
git push
  1. Go to the webpage of your repository, Make a pull request to the original repository and wait for approval by clicking pull request (note: this button is beside compare button, it is NOT New pull request button).

Add yourself

You can add yourself to the page in _people folder just create file name <your_firstname>_<your_lastname>.md in the folder. See the following for the template of the content in <firstname>_<lastname>.md

---
name: Eva Dyer
position: underGradStudent
avatar: eva.jpg
twitter:
joined: 2014
---

<img width="300" src="{{site.baseurl}}/images/people/{{page.avatar}}" data-action="zoom">

### {section_name}
(section content)


Detailed procedures to add yourself:

  1. Prepare your photo, crop it to W:H=1:1.618.
  2. Put your photo to images/people/ folder and name it to <your_firstname>_<your_lastname>.jpg.
  3. Open file _people/<your_firstname>_<your_lastname>.md, change name to your name, position to your position (you can choose position from 4 classes including pi, underGradStudent, gradStudent, researchCoordinator. Position will put you into section that you choose.), avatar to <your_firstname>_<your_lastname>.jpg, joined to the year you joined the lab.
  4. If you have more to tell, you can modify the {section_name} and (section_content) showing in the template. An example would be:
---
name: Eva Dyer
position: underGradStudent
avatar: Eva_Dyer.jpg
twitter:
joined: 2014
---

<img width="300" src="{{site.baseurl}}/images/people/{{page.avatar}}" data-action="zoom">

### Current Project
My current project is about designing a spaceship to prevent alian attack.


  1. Follow Procedure to make change to update the webpage.

note: following sections are out dated and will be updated soon



Add posts

It's very easy to add post. All the posts are located in _posts folder. It arrangement is based on date. Each post can be written in markdown format. You just have to state headers before writing: title, description and categories. description will be shown when you share on social media like Facebook or twitter. See the following headers:

---
title: Summer School in Computational Sensory-Motor Neuroscience (CoSMo)
description: all links to CoSMo summer school in computational neuroscience materials
categories: scientists
---

We have 4 categories: scientists, students, discussion, blog you can choose and this will be rendered to different location.

How to add posts

  • Directly edit on Github, you can simply go to _posts and click New file then put some markdown file e.g. 2016-02-03-post-name.md and start writing blog post. Github also allows you to preview it so it's nice for people who don't want to clone the repo.

  • Clone the repository, kind of the same as directly add post on Github. You just have to clone the repository. Then add new post file, commit and push to the repo.

The changes will take approximately half a minute to render. You can see the new posts or changes on Lemas Lab Group!

Add new publications

All publications from the lab are located in publications.md. Please upload new publication on your own!

Lemas Lab's Projects

ampliseq icon ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

awc_lcms_metabolomics icon awc_lcms_metabolomics

The objective of this study is to develop an automated workflow composition system for LC-HRMS metabolomics data processing.

beach icon beach

The Breastfeeding and EArly Child Health (BEACH) Study

beach-interview icon beach-interview

data analysis for BEACH interview study in 40 pregnant and breastfeeding women in Alachua County

camp icon camp

predicting peptide-protein interactions

ehr-preeclampsia-model icon ehr-preeclampsia-model

Use mom-baby EHR to validate ShinyApp model. The goal of the project is to predict infant delivery for mothers with preeclampsia.

gatorberry icon gatorberry

build a raspberry pi cluster with SLURM installed and assemble viral genome

nlp-perinatal icon nlp-perinatal

this repo contains code for the analysis of perinatal clinical notes

nlp-recipes icon nlp-recipes

Natural Language Processing Best Practices & Examples

omop2obo icon omop2obo

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies

r-demo icon r-demo

space to demo r-packages that can be moved to other projects.

rump icon rump

A Reproducible Untargeted Metabolomics Data Processing Pipeline

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