DoerLBH

Updates of my Life with Wonders~

Contents (a partial summary of Baihan Lin's coding projects)

2016-07-17 posted in [Project]


About me

  • Baihan Lin (林柏翰)
  • University of Washington, Seattle
  • Computational Neuroscience Program
    • Department of Applied Mathematics (B.S. in ACMS)
    • Department of Physics (B.S. in Biophysics)
    • Department of Psychology (B.A. in Psychology)

Research:

  • Baker Lab
    UW Biochem, Institute for Protein Design https://www.bakerlab.org/
    • (2015 Dec) bp_wc2dm (original) -Java- repo
    • (2015 Nov) bp_solver (original) -Java- repo
    • (2015 Nov) bp_creator (original) -Java- repo
    • (2015 Oct) ABEGO_solver (original) -Java / Perl- repo
    • (2015-2016) scripts (original) -Unix cmd / Python- repo
  • Olavarria Lab
    UW Psych, Computational Neuroscience Program
    • (2016 Apr) IntanEphys (original) -MATLAB- repo
    • (2014 May) Patch_Processor_2.0 (original) + (ImageJ) -Java- repo
    • (2014 May) Patch_Processor_1.0 (original) -Java- repo
    • (2014 May) Analysis (original) -Java- repo
  • Teng Lab
    BIME, Virology & Systems Biology
    • (2016 Apr) Ebola_GUI_SL (original) -MATLAB / R- repo
    • (2014 Aug) Matrix_solver (original) -Java- repo
    • (2014 Jul) Influenza_Model (original) -MATLAB-
    • (2014 Dec) PCA (original) -R-
  • Qian Lab / Huang Lab
    UW Amath, Institute for Systems Biology
    • (2016 July) GRN (original) -R- repo
    • (2016 July) SPADE_stochastics (modify) -MATLAB- repo
  • BGI
    Genomics, Human Health Application Lab http://www.genomics.cn
    • (2013 Sep) Autism_Genomics_QC_report_adapter (modify) -Perl- repo
    • (2013 Aug) Autism_Genomics_QC_NACTG_stat (original) -Perl- repo
    • (2013 Jul) scripts (original) -term cmd-
  • Comp Neuro
    • (2014 Feb) Neuronal_RC_HH_Model (original) -MATLAB- repo
    • (2014 Jan) Neuron_Tuning_Curve (original) -MATLAB- repo
  • Indie
    • (2016 Apr) Energy_plot (original) -MATLAB-
    • (2016 Mar) Ebola_Bat_Model (original) -MATLAB- repo
    • (2016 Mar) Rika_Model (original) -MATLAB-
    • (2016 Feb) Redo_NuRsE (modify) -MATLAB- (from jianxigao, learn the methodology) repo
    • (2016 Feb) Biochemical_Oscillation (original) -MATLAB- repo
    • (2015 Dec) Network_Analysis (original) -MATLAB / R / Cytoscape-
    • (2015 Nov) nextflu (modify) -Python- (from blab, investigate how it work) repo
  • Old
    • (2014 Jun) Hoffman_Coding (original) -Java- repo
    • (2011 Jul) Hospital_Management (original) -C-

Engineering:

  • 3DPrint https://github.com/doer3Dprint
    UW WOOF3D 3D printing club http://students.washington.edu/woof3d/bigblue.html
    • (2016 Mar) BigBlue3DPrinter (modify) -C- (from Marlin Firmware, modified to fit UW Big Blue) repo
    • (2016 Feb) Octoprint (modify) -JavaScript- (from fossel, modified to enable wifi printing in UW Big Blue) repo
    • (2016 Feb) Smoothieware (modify) -C++- (from Smoothieware, modified to fit UW Big Blue) repo
    • (2016 Feb) MarlinForKilo (modify) -C- (from pomeroyb, to learn which parameters to change) repo

Idea:

  • Roadmap (original)
  • Simplified_Social (original)
  • iOS_Quick_Tracker (original)
  • File_Reminder (original)

Web:

Learn:

  • GitHub - gotgithub (forked)
  • R - bgiR (forked)
  • Rosetta - rosetta_clone_tools (forked)
  • TED - TED视频 (forked)

Life:

  • ElseBand (original) FB_page Youtube
  • WhateverBand
  • Life-Time-Tracker (clone) (forked from zhangmhao)

Contact:


Baihan Lin
Computational Neuroscience Program
University of Washington

Emails:

  • (Work) doerlbh@gmail.com,
  • (Edu) sunnylin@uw.edu

Skills:

  • (Proficient) Java, MATLAB
  • (Familiar) Perl, C/C++, R, Unix cmd, Python
  • (Learning) Mathematica, Python, HTML, JavaScript, CSS, PHP

Environment: Windows, Apple OS, Linux, BOINC, Hyak

2016-06-20

2016-07-08 posted in [Day]

March into Gene Regulatory Network.

2016-06-20

2016-06-20 posted in [Day]

NeuroFutures Conference 2016

2016-05-16

2016-05-16 posted in [Day]

another productive day in preparing for gene-editing and protein design.

Interesting Papers for later

2016-05-14 posted in [Paper]

doi:10.1126/science.aad7701 PMC: PMID:

Paper - Characterizing the transmission dynamics and control of ebola virus disease

2016-03-12 posted in [Paper]

Chowell, G. & Nishiura, H. Characterizing the transmission dynamics and control of ebola virus disease. PLoS Biol 13, e1002057, doi:10.1371/journal.pbio.1002057 (2015).

Paper - Inference and forecast of the current west african ebola outbreak in Guinea, sierra leone and liberia

2016-03-11 posted in [Paper]

Shaman, J., Yang, W. & Kandula, S. Inference and forecast of the current west african ebola outbreak in Guinea, sierra leone and liberia. PLoS Curr 6, doi:10.1371/currents.outbreaks.3408774290b1a0f2dd7cae877c8b8ff6 (2014).

Paper - Early transmission dynamics of Ebola virus disease (EVD), West Africa, March to August 2014

2016-03-10 posted in [Paper]

Nishiura, H. & Chowell, G. Early transmission dynamics of Ebola virus disease (EVD), West Africa, March to August 2014. Euro Surveill 19 (2014).

Paper - Dynamics and control of Ebola virus transmission in Montserrado, Liberia - a mathematical modeling analysis

2016-03-09 posted in [Paper]

Lewnard, J. A. et al. Dynamics and control of Ebola virus transmission in Montserrado, Liberia: a mathematical modelling analysis. Lancet Infect Dis 14, 1189-1195, doi:10.1016/S1473-3099(14)70995-8 (2014).

Paper - Mastering the game of Go with deep neural networks and tree search

2016-03-08 posted in []

Paper - Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction

2016-03-07 posted in [Paper]

Paper - How to escape the cancer attractor - Rationale and limitations of multi-target drugs

2016-03-06 posted in [Paper]

Paper - Transmission dynamics and control of Ebola virus disease (EVD) - a review

2016-03-05 posted in [Paper]

Paper - An IDEA for short term outbreak projection - nearcasting using the basic reproduction number

2016-03-04 posted in [Paper]

Paper - The basic reproductive number of Ebola and the effects of public health measures - the cases of Congo and Uganda

2016-03-03 posted in [Paper]

Paper - Poincaré, celestial mechanics, dynamical-systems theory and “chaos”

2016-03-02 posted in [Paper]

Paper - Experimental and Modeling Study of Oscillations in the Chlorine Dioxide Iodine Malonic-Acid Reaction

2016-03-01 posted in [Paper]

Paper - Combining flux and energy balance analysis to model large-scale biochemical networks

2016-02-29 posted in [Paper]

Paper - Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes

2016-02-28 posted in [Paper]

Paper - Linear analysis near a steady-state of biochemical networks (control analysis, correlation metrics and circuit theory)

2016-02-27 posted in [Paper]

Paper - The chemical master equation approach to nonequilibrium steady-state of open biochemical systems

2016-02-26 posted in [Paper]

Paper - Stochastic phenotype transition of a single cell in an intermediate region of gene state switching

2016-02-25 posted in [Paper]

Paper - Anticipating critical transitions

2016-02-24 posted in [Paper]

Paper - Universal resilience patterns in complex networks

2016-02-23 posted in [Paper]

Launch "A Paper A Day" Plan

2016-02-22 posted in [Paper]

Random

2000-01-01 posted in []