Setting up Biopython

http://www.codesdope.com/python-introduction
Open IDLE
When running a new file and trying to add it to the old code (if you have a new code that you are messing up, but you don't want to screw up your old code with all this clutter of failures, you create a new file and then

In python you have color code schemes
Keywords (orange):
'False', 'None', 'True', 'and', 'as', 'assert', 'break', 'class', 'continue', 'def', 'del', 'elif', 'else', 'except', 'finally', 'for', 'from', 'global', 'if', 'import', 'in', 'is', 'lambda', 'nonlocal', 'not', 'or', 'pass', 'raise', 'return', 'try', 'while', 'with', 'yield'

Outputs (blue): 
Anything you write after print 

This will be the output:

In order to have a command executed to create an output you need the >>> you cannot have anything run if you just run it like this

 

You can write a new code here in a new file of IDLE, have it not run bc it has no arrows, then while in the new tab you click on run, up at the top there, then click on run module, it will ask you to save it, save it. Then it will run it in the main IDLE tab that runs all your instructions.  

To make a comment you need a # an then a comment, it will appear in red and it will not affect your code, it's just instructions for yourself. 

You can define variables and then manipulate them with commands making them add, subtract, divide or multiply. 

There are certain words that you cannot make variables, these are keywords and they appear in orange. Each one has a different function in python. 

You can get the code to identify what you are inputting (I don't understand the use of this yet). If you write, type and then a word, it'll identify it as string or str, if you write a number it'll say integer or int, if you write a decimaled number it will write float. 

Issues: because the website I am using to learn to code is made for python 2 and not python 3, some of the commands and syntax and just general rules for coding have been changed. So as I try to complete the excercises the website gives me, I need to modify the code and it takes many trial and errors before I manage to get it to complete the function I want it to. What I am currently trying to figure out is how to solve these two function because I've been working on getting them to work for the past hour and reading articles about the changes from 2 to 3 and I can't figure it out. 

https://docs.python.org/3.0/whatsnew/3.0.html

What has changed in python from 2 to 3. 

Help for beginner functions (colors) http://www.annedawson.net/Python3_Intro.htm
http://www.annedawson.net/Python3Programs.txt (example programs)

Progress report 3

https://docs.google.com/presentation/d/1dQfjkiDvQALoH287uLhs4TDPdfTRDmXyto4qvGHUdmk/edit#slide=id.g1a0be35812_0_23

Including Protein Structure and Docking sites in Website (RaptorX)

RaptorX is a free downloadable program which predicts the 3D protein tertiary model as well as possible binding sites. It also allows you to compare 2 or more protien structures through protein structure alignment. You send in your sequence (job) and then they will send you back "its secondary and tertiary structures as well as contact map, solvent accessibility, disordered regions and binding sites." In order to download the software you must be affiliated with an organization. Since I am not, after I have designed my website I need to "please send us your name, organization and your email address through contact us and we will do some internal setup so that you can download the software." 
Official Website: 
http://raptorx.uchicago.edu/
User guide: 
https://www.oregon.gov/OMD/OEM/docs/plan_train/RAPTOR/RAPTOR_User_Guide.pdf
Protein structure, modeling and applications:
https://www.ncbi.nlm.nih.gov/books/NBK6824/

ProDy:
https://pypi.python.org/pypi/ProDy/1.8.2

Matlab Bioinformatics

The MatLab bioinformatics is a toolbox which includes modules which allow you to read information from FASTA, SAM, CEL, CDF files. You can also access information GenBank and NCBI Gene Expression Omnibus. The program can open the files and then present the data found within the files as visuals ( sequence browsers, spatial heatmaps, and clustergrams). It also has "statistical techniques for detecting peaks, imputing values for missing data, and selecting features" 

After reviewing the overview of the bioinformatics program on MatLab, I have come to the conclusion that it would be no help to me. The primary purpose of the program is to allow scientists to input their data, code for how they'd like the program to organize the data and then analyze the data. This would help the scientist come to conclusions about the data faster than had they just looked at completely unorganized data. Also helps them detect trends. I am not trying to analyze data at this point. I am trying to collect all the proteins functions and place them in one place. Later on, once I have designed the website I could use Matlab to analyze all the data I've collected and come to a conclusion myself. Scientists would ideally go through and take all the data I've compiled and then organize it themselves and come to a conclusion themselves. I am just the mediator, I allow them to access all the data in one place and then they analyze it. 

What I take from this: I need to include the protein sequence in a FASTA file so that if researchers do what to put my data into MatLab and analyze the trends they can. 

Process for strain name retrieval

1. Go onto Science direct
2. Click on the button for Bronx Science proxy
3. Search subspecies name borrelia... in this order

Borrelia burgdorferi

Borrelia garinii

Borrelia afzelii 

Borrelia bavariensis

Borrelia valaisiana

Borrelia lusitaniae

Borrelia filandensis

Borrelia bissettii 

Borrelia spielmanii

Borrelia carolinensis 

Borrelia kurtenbachii 

Borrelia andersonii

Borrelia americana 

Borrelia turdi 

Borrelia yangtze 

Borrelia japonica 

Borrelia chilensis 

Borrelia parkeri

Borrelia duttonii 

Borrelia hermsii

Borrelia turicatae

Borrelia recurrentis 

Borrelia crocidurae 

Borrelia mayonii 

Borrelia persica 

4. Click on every link that has both keywords in it (Borrelia+subspecies name) 

5. Go to the page of the link and see if it is the full article (it should be since I have full access to the database)

6. Scroll down and look for the chart or pictures where it lists every strain used in the study. It will list both the strain and the subspecies (genospecies) the strain is apart of. 
7. In order to identify whether the chart holds strain, look for key words like strain name, or species and isolate, or just isolate. 
8. Copy any data in the column under the key words, if it split up by species then make sure you record them under the specific species. 

7. Go onto my master list of strains and then find the subspecies that the strain you have found is listed under. Scan to see whether you have already collected that strain name. 

8. If you have not yet collected that strain, copy it down under the proper subspecies. 

9. Do this for every paper that includes the subspecies in it's title when you search it. 

10. While going through the papers, if the chart includes a new subspecies that you don't have on your master list, add it to the master list along with any strains that fall under its category. 

Progress report 2

https://docs.google.com/presentation/d/1URbdIgvTztwPtwtl2RHybWTiGNr_l4IEVECbvlAYRZQ/edit

Literature+Prior Arts Survey

Prior Arts Survey
http://opm.phar.umich.edu/species.php?species=Borrelia%20burgdorferi
This database contains the structure and information on OspC protein of Borrelia burgdorferi

http://borreliabase.org/
This database contains multiple DNA sequences of the strains.

http://www.lyme-disease-research-database.com/
Database of technical papers on lyme disease.

http://biopython.org/
I will be using biopython to design my website

https://www.ncbi.nlm.nih.gov/pmc/
I get my information from PubMed papers

http://www.sciencedirect.com/
I get my information from technical papers on science direct along with PubMed


In order to figure out what a patent currently exists for, I first needed to figure out the different parts of my project that would be patentable. So first, a database on lyme disease related things. There are only 3 that exist and both are listed above, neither of them cover the territory that my database will. Second would be the sequences or the strains that I am collecting. According to a recent supreme court decision, sequences that exist in nature cannot be patented but sequences that are edited and are not found in nature can be patented. This will not be an issue for me because I am only using the natural genomes of Borrelia. Next in terms of patenting strains, you can only patent a strain if it does not exist in nature and you genetically engineered it. I will not be dealing with any genetically engineered strains. Nor am I creating any sort of lyme disease strains therefore a patent search in order to avoid infringing on someone else's patent would be pointless. I will be coding in a language that is free to public use and if I decide to use Matlab, we have paid for a years subscription so that won't be an issue. I looked through about 25 patents under the input bioinformatics lyme disease as well as database lyme disease and nothing that would overlap with my research came up. Most patents under that search were patenting a antibody which would detect lyme disease proteins in a western blot or a new type of antibiotic. I am not creating anything, only compiling existing data that is already available to the public so I do not see any part of my project that would infringe upon a patent.

Literature Survey
https://www.ncbi.nlm.nih.gov/pubmed/27588694
FlgE is a protein involved in the Borrelia hooking onto cells.

https://www.ncbi.nlm.nih.gov/pubmed/26480895
BbHtrA is a protease within Borrelia burgdorferi.

https://www.ncbi.nlm.nih.gov/pubmed/26438793
OspC is an outer surface protein on Bb which prevents it from being eaten by phagocytes.

https://www.ncbi.nlm.nih.gov/pubmed/26953324
OspA and OspB are both outer surface proteins on Bb and help it evade the immune system

https://www.ncbi.nlm.nih.gov/pubmed/27502325
Ip28-1 plasmid is responsible for the variation in the VIsE lipoprotien that helps Bb evade the immune system.

https://www.ncbi.nlm.nih.gov/pubmed/27161310
A variant of TP0435 lipoprotein which was thought to be found only within Treponema pallidum is found within Borrelia Burgdorferi and it allows the bacteria to adhere to a host cell.

https://www.ncbi.nlm.nih.gov/pubmed/26808924
BBK32 is another lipoprotein which blocks the recruitment of molecules within the complement system

https://www.ncbi.nlm.nih.gov/pubmed/26434356
BGA66 and BGA71 are both outer surface proteins which inhibit the complement system, the alternative pathway and the classical pathway.

https://www.ncbi.nlm.nih.gov/pubmed/26247174
Lmp1 aids in the adhesion of Bb to the host cell and allows the persistence of infection.

https://www.ncbi.nlm.nih.gov/pubmed/26181365
BAPKO_0422 is a protein that binds to the human factor H and inhibits the complement system. 

https://www.ncbi.nlm.nih.gov/pubmed/24191298
CspA binds to human factor H and inhibits the complement system. 

https://www.ncbi.nlm.nih.gov/pubmed/27725820
CspZ, ErpA, ErpC, ErpP, and p43 are all surface proteins that allow Bb to evade the immune system. Varient of CD59 binds to human factor H to inhibit complement system.

https://www.ncbi.nlm.nih.gov/pubmed/24702793
CspZ binds to CFH and CFHL-1 to inhibit complement system. CspZ is one of the 5 proteins that Bb creates that binds to CFH and CFHL-1.

https://www.ncbi.nlm.nih.gov/pubmed/25582082
ErpA, ErpC, ErpP all bind to CFH and CFHL-1 however ErpC may only bind to CFHR and not CFH.

https://www.ncbi.nlm.nih.gov/pubmed/20022381
CRASP-1/Bba68 works with OspE to bind to factor A and inhibit complement system.

https://www.ncbi.nlm.nih.gov/pubmed/14629271
p39, p41 in IgM IB, and p83/100, p39, Osp17 in IgG IB; in late LB: p39, p41 in IgM IB, and p83/100, Osp17, p21 and p43 in IgG IB are all proteins that can be detected at different stages during a lyme disease infection.

https://www.ncbi.nlm.nih.gov/pubmed/11599789
Osp17 and OspC actually induce a humoral immune response  

https://www.ncbi.nlm.nih.gov/pubmed/19451251
CspA a surface lipoprotein binds to FH/FH-1 (human factor H and H like protein) and allows Borrelia to evade the immune system in an unknown manner. FH aids in the immune system by binding to defect human cells and marking them for destruction. 

Borrelia Burgdoferi evades the immune system by preventing certain pathways of the immune response to work. It inhibits the complement system by creating proteins that bind to the human factor H as well as CHF and CHFL-1. These prevent the complement system from from recruiting other proteins to fight the infection. The proteins that bind to human factor H are a variant of CD59, variant of TP0435, BBK32, BGA66, BAPKO_0422, CspA and BGA71. Other proteins aid in the adhesion of the bacteria to the host cell, these include: Lmp, FlgE. The detection of lyme disease is different depending on how far the infection has progressed. In the earliest stages p39, p41 in IgM IB, and p83/100, p39, Osp17 in IgG IB. In late LB: p39, p41 in IgM IB, and p83/100, Osp17, p21 and p43 in IgG IB. It is crucial that we understand what proteins to detect at different stages so that we can have the most accurate test to see whether or not you have lyme disease. The current test is only 50% accurate. Knowing which proteins are present at which stages and which proteins do what will help researchers find better ways to treat and diagnose lyme disease.