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[C-bCM-S]: Computational (Bio)Chemical & Molecular Systems
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 C-bCM-S: Computational (Bio)Chemical

& Molecular Systems [⋆⋆] 

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This topic will explore 2D/3D structural modelling & functional interactions simulations, pertaining to molecular mechanisms in biochemical and bionanotechnological systems. This section is not exclusively related to Neuroscience (synaptic dynamics, neuronal metabolism, neural electrochemistry, neurogenetics, etc). The reason why there it is more focused on Neuroscience is because I have more expertise with this subject, and I will expand to other subjects soon.

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Bioinformatics and Neuroinformatics Data Analysis (e.g. using open-source databases)

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Comparative NeuroInformatics (using, for example, Allen Brain Mapping BioArrays)

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Project Fields:​ Cellular Genetics Data

Description: xxxxx

My Work & Contributions: xxxxx

Collaborations/Feedback: xxxxx

Location Activities: Home-based

Status/Timeline: 2016-2017; not yet analysed using Machine Learning.

s

Other Links to external sources:

Data sources:

--- http://www.brain-map.org/api/index.html

--- http://alleninstitute.github.io/AllenSDK/

--- http://connectivity.brain-map.org/

--- http://human.brain-map.org/microarray/search

--- http://human.brain-map.org/ish/search/?page_num=0&page_size=400&no_paging=false&search_term=&search_type=subcortex&

--- http://mouse.brain-map.org/search/show?page_num=0&page_size=20&no_paging=false&domain1=8&domain2=1080&domain1_threshold=0,50&domain2_threshold=1,50&image_set=P56&search_type=differential

--- http://www.alleninstitute.org/legal/terms-use/

--- https://www.youtube.com/user/AllenInstitute

 

 

Hardware: Intel Quad Core i7 & Celeron Computers

Operating Programs & Software Tools: MS Win 10 OS;  Web-based Allen Brain BioArrays

Programming Languages: xxxxx

Coding Elements:  xxxxx

Computational Techniques: xxxxx

 

Link to Programming Code Files:

Public (full open access) (Google Drive Cloud and GitHub): https://drive.google.com/drive/folders/0B0qSKFqszohLTTZIZkg1c09xaVU?usp=sharing

Private (shared password-protected) (Google Drive Cloud): xxxxx

File types: xls csv

​License: xxxxx

 

Hippocampus vs Prefrontal Cortex, Auto-Generated Data.

 

--- probes_hm1.csv [11 x 2000 matrix] (238KB)

--- expression_hm1 [40 x 2000] (625KB)

 

Base Math Coding & Program Computations & System (Diagrammatic):

XXXXX

 

Images:

Original Data by Others, Content Manipulation by Me, Screenshots by Me.

 

Video Embeds: xxxxx

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BioInformatics (e.g. Allen data)
Molecular Modelling

Molecular Modelling (VMD & PyMol)

 

VMD & PyMol

 

PyMol
https://www.schrodinger.com/pymol
https://pymolwiki.org/index.php/Main_Page
https://sourceforge.net/projects/pymol/

Computational Molecular Biophysics at University of Illinois (USA)
Visual Molecular Dynamics
http://www.ks.uiuc.edu/Research/vmd/
http://www.ks.uiuc.edu/Publications/Papers/
https://www.sciencedirect.com/science/article/pii/0263785596000185

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bioc5
bioc7
bioc6
bioc8
Electro-Dynamics Biophysics (NEURON)

Electro-Dynamics/BioPhysics - 'NEURON' Software - Construction of Neurons

 

​Neuronal Molecular Electro-Dynamics (using NEURON-DB)

 

Project Fields:​ xxxxx

Description: t xxxxx

My Work & Contributions: User-Interface Level; Code Dev. Edit to sodium concentration and effects on AP.

Collaborations/Feedback: xxxxx

Location Activities: Home-based

Status/Timeline: xxxxxx

 

Other Links to external sources:

--- https://www.neuron.yale.edu/neuron/static/py_doc/index.html

--- https://neuroml-db.org/

--- https://www.neuroml.org/NeuroMLValidator/Samples.jsp

--- https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=114394&file=/NN_kole/nax.mod#tabs-1

--- https://www.nature.com/neuro/journal/v11/n2/full/nn2040.html (Na+ channel dependence of AP initiation in cortical pyramidal neuron (Kole et al. 2008))

--- https://senselab.med.yale.edu/modeldb/HowToCite.cshtml

 

Hardware: Intel Quad Core i7 & Celeron Computers

Operating Programs & Software Tools: MS Win 10 OS;  NRNIV, .NET

Programming Languages: (can use  C++ and NeuroML for native)

Coding Elements:  xxxxx

Computational Techniques: xxxxx

 

Link to Programming Code Files:

Public (full open access) (Google Drive Cloud and GitHub): https://drive.google.com/drive/folders/0B0qSKFqszohLTTZIZkg1c09xaVU?usp=sharing

Private (shared password-protected) (Google Drive Cloud): XXXXX

File types: nrniv, hoc, mod, nml

​License: xxxxx

 

--- initiate_neuron_hm1.hoc (288 lines of code) (6KB) (= Initiation)

---  nax_hm1.mod (149) (4KB) (= Sodium Ions)

---  A3+AIS_original_hm1.hoc (15041 lines) (541 KB) (554,050bytes) (= Defining all values for all dendrites and axons)

 

Base Math Coding & Program Computations & System (Diagrammatic):

 

Images:

Content Files Manipulated by HM, Screenshots by HM

 

Video Embeds: xxxxx

2017-10-04 (3)
2017-10-04 (2)
2017-10-03 (25)
2017-10-03 (10)
2017-10-03 (23)
10_large_subunit (biochemistry software)
Isat 3d graph
2017-10-04 (8)
2017-10-04 (3)
2017-10-04 (2)
2017-10-03 (25)
2017-10-03 (10)
2017-10-03 (23)
Other

Potential Future Working Contributions to Other Projects related to the following:

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Other 

 

Other future works will be related to these other external independent projects by other people/organisations listed below.

 

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Here is a new list :

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â–º https://sites.google.com/site/bioneurotech/-repo-2

â–º https://docs.google.com/document/d/1Nv6BimGLFgvbSYeNQZO5Cjna_iWcquwoF47MMsll5fA/edit?usp=sharing

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List B:​

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--- STochastic Engine of Pathway Simulation (STEPS) (https://github.com/CNS-OIST/STEPS)

Uses: C++ compiler (supporting c++11), Python 2.7+ (+ NumPy), CMake, Cython, SWIG, BLAS/OpenBLAS (http://www.openblas.net/)

​--- Diagrammatic Visualisation of Interaction Mechanisms Data

​--- Gepasi3/Copasi Biochemical System Simulator (http://www.gepasi.org/)

​--- 3D visualisation

--- NFSim (Network-free stochastic simulator)

--- NeuroRD (Java, XML to run model spec)

--- JARNAC – a system of enzymatic metabolism simulation

--- ZigCell3D – intracellular 3D dynamics and reaction networks, visualisation and functional modelling framework

--- Arena3D – visualisation of biological networks in 3D

--- OpenMM – micromolecular

--- http://bivi.co/development-status/under-development-not-released

--- Systems Biology Markup Language - http://sbml.org/Downloads

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638623/

BioModels.net; LibSBML Editor; MOCCASIN; SBMLToolbox

--- (TBC) Protein Folding software (folding.stanford.edu)

--- Proteopedia.org – 3D visualisation and annotation of nucleic acids and proteins readouts

--- Zooniverse.org

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​The work above will have significant impacts in the following fields:

--- Biomolecular Engineering & Cellular Pathophysiology (Computational Approach)

--- Modelling computational structural biochemistry (inspired by Michael Levitt's work which won him the 2013 Nobel)

--- How can this be applied to: genetic engineering, gene therapy and stem cell technologies.

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Biological Informatics extra info:

--- Work in biomolecular information systems, and dynamic complex cellular physiological systems. This is not strictly directly-related to genomics.

​--- http://www.bioinformatics.org/people/index.php?user_hash=669fde98787fad72

(H Muzart, member profile)

--- https://crcns.org/data-sets (collaborative data-sharing in computational neuroscience)

--- http://connectivity.brain-map.org/transgenic  (Allen Institute 3D and 2D atlases for histological sub-structures of brain and relation to gene expression/knockouts +/+, +/-, -/- ) (privately-funded and govn-funded US project)

--- http://www.biometrics.tibs.org/  

--- http://www.neb.uk.com/Product_Overview/CellImagingOverview.asp  (New England BioLabs - Spring Harbor - products for projects)

--- http://journals.plos.org/ploscompbiol/s/latex  (PLoS Comp Biol data forms)

​--- [TBC] BioMedComms - finding a way for data to be communicated and used in translational clinical applications. BioNeuroSoft - a base operations infrastructure for BioMedComms.

 

​Open-Source Bionanotechnology

​--- Another project requiring more research will be the Nano-Systems Repository (a OA repository of bionanotechnology systems --- DIY nano-machines, molecular computing, dot cellular automata, chem tech, biochem tech)

 For each of these, there will be information on:

--- Blueprints for the complete nano-system

--- Their functional algorithm(s) and interaction(s) with other nano-systems

--- The algorithm for manufacturing the nano-system from raw parts to end product

 

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Images:

https://commons.wikimedia.org, File:10_large_subunit.gif, CC-BY(URMSC)

10_large_subunit (biochemistry software)
VIR-576

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