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Name: Silvia Talavera Marcos

Type: User

Bio: Biochemistry graduate. Bioinformatics MSc. PhD student. Interested in genomics, microbiology and health.

Twitter: silvtal

Welcome to my GitHub page!

I'm Silvia, a PhD student at the Autonomous University of Madrid, Spain . I'm currently working on my doctoral thesis on microbial community assembly at Aguirre de Cárcer's lab

🔭 My work includes ...

Programming protocols for automating microbial cultures 🌱
Analyzing microbial community networks 🕸️
Identifying and exploring functional core groups in a community 🔎
Studying pangenomes and metabolic modeling 🧪

💻 Things I code with

👯 I’m looking to collaborate on ...

Software development and benchmarking 👩‍💻
Studying microbial assembly 🦠
With people all around the world! 🌎

📫 How to reach me

📧 [email protected]
📍Now on a stay at The University of Tokyo 🇯🇵 (#601 Iwasaki Lab, Bioscience Bldg)
🗣️ You can talk to me in Spanish, English and Japanese. Learning Norwegian and French ☺

️

Welcome to Tokyo!

Above are the last 3 pictures posted by @tokyotokyooldmeetsnew!
Currently, the weather is: °C,
Today, the sun rises at and sets at .

This README file self-updates every 3 hours
Last refresh: Wednesday, 6 September, 18:47 CEST
Here's how it works

Silvia Talavera Marcos's Projects

carveme

CarveMe: genome-scale metabolic model reconstruction

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

correlation_graphs

Based on Goyal et al.'s recently published method for inferring statistically significant correlations between OTUs (https://www.biorxiv.org/content/10.1101/2021.01.04.425224v1)

custom_ot2_utils

Opentrons OT2 robot functions or custom labware definitions that we feel other people might find useful

This package includes command line scripts and standalone R/c++ functions for simulating growth-dilution experiments. These simulations include neutral drift and optionally functional groups with different group fitness.

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

get_core_reactions

Given a folder with eggnog annotation files (multiple genomes), create a consensus annotations file and save a series of core reactions in different formats

microbeannotator

Pipeline for metabolic annotation of microbial genomes

ntinfo

ntinfo includes functions similar to those of CUSP and the Reverse Complement online tool. This script also comes with a supplementary GUI (ntitk.py). Saved as a .lnk file, everything is just a click away (including help).

oncosimul

phyloassembly

Code for: Leveraging phylogenetic signal to unravel microbial community function and assembly rules

predicting_fixation

rstoolbox

Python Toolbox For Rosetta Silent Files Processing

sbml_to_graph

A few rudimentary functions to generate metabolite graphs from SBML models. Uses ReFramed and one CarveMe function.

silvtal

silvtal.github.io

Personal website

spent_media

spyder-cyberpunk-color-theme

A good old magenta+cyan cyberpunk theme for Python syntax coloring in Spyder

tfm

Este repositorio recoge los scripts desarrollados para automatizar los análisis correspondientes al Trabajo de Fin de Máster "Modelización metabólica de comunidades microbianas estables crecidas con fuentes de carbono y energía únicas y simples" (Silvia Talavera Marcos, Máster en Bioinformática y Biología Computacional, Universidad Autónoma de Madrid).

tnseq_read_simulation

Reads simulation and analysis following the alternative method proposed at https://journals.asm.org/doi/full/10.1128/mSystems.00976-20# (Fig 1, right)

wordle-jp

Japanese adaptation of Josh Wardle's Wordle