User:Boris

Boris Steipe  (course coordinator)

Medical Sciences Building, Room 5279

Toronto, Ontario      M5S 1A8

T: 416-946-7741

E: boris.steipe@utoronto.ca

Resources

 

Extension and Template syntax

 

Original sidebar links;

• Special:RecentChanges
• Help:Contents
• What links here ... ctrl - option - j
• Related Changes ... ctrl- option - k
• Special:Upload
• Special:SpecialPages

Service pages

• MediaWiki:Common.css
• MediaWiki:Sidebar
• Multi Boiler Plate extension drop down menu (Copy Template location from there to edit.)

 

Current

• Workshops
• User:Boris/Temp
• Test
• Redlink

"NOX1 NADPH oxidase 1 [Homo sapiens (human) - Gene - NCBI"]. http://www.ncbi.nlm.nih.gov/gene/27035. Retrieved 2015-12-21. 

 

Test

Media:Test.txt

Syllabus snips

Coordinator

Boris Steipe

 

Instructor

Boris Steipe

 

Contact

All contact will be via a Google group.

• To send mail, click here: mailto:bch441_2017.
• To visit this forum on the Web, click here: BCH441_2017.
• Note that this is a list for technical discussions and I expect everyone to follow the standards of communication spelled out here: FND-Netiquette.

 

Contact

Course communication will take place on the Quercus discussion section. We'll see how this goes. If it's not suitable for our needs we'll find an alternative.

 

Office hours

(Virtual) face to face meetings are by appointment, if required. However, we will be able to resolve almost all issues by e-mail. You will find that discussions by e-mail are both more efficient and effective than meetings. Moreover e-mail discussions leave you with a document trail of what was discussed, can contain links to information sources, and we can share points of general interest more easily with the class.

 

Student Wiki

Many of the class activities will take place interactively on a separate Wiki site (the "Student Wiki"). You will create a personalized user page there, and use it to submit materials as required.

This Wiki is not accessible to the general public, you need an account that we will register in the first class-session.

 

 

... under development

CSB map 2

Week	prereading	topic	exercise	quiz
00	-	Intro; what is a system; topic for the term: extract systems from data; Organization; Prerequisites	Exercise	quiz
00	-	A project: what do we need to solve this problem	Exercise	quiz
00	-	A Software project; defining project; defining tasks; infrastructure	Exercise	quiz
00	-	Biological entities	Exercise	quiz
00	-	Dynamics	Exercise	quiz
00	-	Annotations	Exercise	quiz
00	-	Relationships	Exercise	quiz
00	-	Systems discovery	Exercise	quiz
00	-	Visualization	Exercise	quiz
00	-	Interpretation	Exercise	quiz
00	-	Results	Exercise	quiz
00	-	Results	Exercise	quiz

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CSB map

00	prereading	topic	exercise
01	-	Intro	Wiki
02	Annotation	Web	GO, GOSemSim
03	prereading	Gene lists	FAA, GSEA
04	prereading	Genome, transcriptome	GEO (4+5)
05	prereading	Proteome, Metabolome	GEO 2?
06	prereading	Graph theory	exercise
07	prereading	Interactome	exercise
08	prereading	Networks	exercise
09	prereading	Systems extraction	exercise
10	prereading	Dynamics	exercise
11	prereading	Modelling	exercise
12	prereading	Synthetic biology	exercise

• User:Boris/Temp/APB - Applied Bioinformatics page hierarchy

• User:Boris/Temp
• (Computing with PDB file, originally A4)
• (Phylogenetic analysis, long version)

• Cargo Cult Bioinformatics
• VMD tutorial(s)
• R tutorial
• Aminoacid tutorial
• Stereo Vision tutorial
• Database Identifiers
• Integrated_Exam_Questions

Additional BIO Topics

• Must make note to alert students who run LINUX boxes that some assignment tasks can be conveniently Perlified.
• http://www.biosolveit.de/PoseView/

Additional CSB Topics

http://www.elsevier.com/wps/find/bookdescription.cws_home/707460/description

• Elsevier - Introducing Computational Systems Biology
• Elsevier - Enabling Information and Integration Technologies for Systems Biology:
  • Elsevier - Databases for Systems Biology.
  • Elsevier - Natural Language Processing and Ontology-enhanced Biomedical Literature Mining for Systems Biology
  • Elsevier - Integrated Imaging Informatics
  • Elsevier - Simpathica: A Computational Systems Biology Tool within the Valis Bioinformatics Environment
  • Elsevier - Standards, Platforms and Applications
• Elsevier - Foundations of Biochemical Network Analysis and Modeling
  • Elsevier - Introduction to Computational Models of Biochemical Reaction Networks
  • Elsevier - Biological Foundations of Signal Transduction and the Systems Biology Perspective
  • Elsevier - Reconstruction of Metabolic Network from Genome Information and Its Structural and Functional Analysis
  • Elsevier - Integrated Regulatory and Metabolic Models
• Elsevier - Computer Simulations of Dynamic Networks
  • Elsevier - A Discrete Approach to Network Modeling
  • Elsevier - Gene Networks: Estimation, Modeling and Simulation
  • Elsevier - Computational models for circadian rhythms: Deterministic versus stochastic approaches
• Elsevier - Multi-Scale Representations of Cells and Emerging Phenotypes
  • Elsevier - Multistability and Multicellularity: Cell Fates as High-dimensional Attractors of Gene Regulatory Networks
  • Elsevier - Spatio-Temporal Systems Biology
  • Elsevier - Cytomics—from cell states to predictive medicine
  • Elsevier - The IUPS Physiome Project: Progress and Plans.

Additional APB Topics

• • GPU and Cloud computing
  • CSS ( http://www.csszengarden.com/ , http://en.wikipedia.org/wiki/Help:User_style , )
  • REST as API. Programming example: SADI or BOLD (Barcode of life).
  • GO annotation in http and R

Practice to think

Repository

• Many hard logics questions here at Quora
• get to an island with two short planks.
• If two guns are pointed EXACTLY at each other, are mounted horizontally and the bullets leave the barrel at the same time then the bullets will collide regardless of muzzle velocity. The reason is that the vertical component of the acceleration will be equal.
• If you walk up and down a mountain, will you be at the same spot on the same hour?
• Three light switches: test which one switches with only one try.
• A scientist flies from his base ... what color is the bear?
• The three doors of the gameshow
• You are travelling down a road to a village. You reach a fork in the road and find a pair of identical twin brothers standing there. One of the brothers always tells the truth and the other always lies. If you are allowed to ask only one question to one of the brothers to find which is the correct road to the village, what is your question ?
• A boat has a ladder that has six rungs, each rung is one foot apart. The bottom rung is one foot from the water. The tide rises at 12 inches every 15 minutes. High tide peaks in one hour. When the tide is at its highest, how many rungs are under water?
• three glasses with OJ, three with water. Move only one glass so that full and empty alternate
• You are given two candles of equal size, which can burn 1 hour each. You have to measure 90 minutes with these candles. (There is no scale or clock). Also you are given a lighter.
• Can you name three consecutive days without using the words Wednesday, Friday, or Sunday?
• A murderer is condemned to death. He has to choose between three rooms. The first is full of raging fires. The second is full of assassins with loaded guns. The third is full of lions those haven't eaten in 3 years.
• If you were alone in a dark cabin, with a petroleum lamp, a fireplace, and a candle but you have only one match, which would you light first?
• You are driving along in your car on a wild, stormy night, it's raining heavily, when suddenly you pass by a bus stop, and you see three people waiting for a bus: an old lady who seems to be having a heart attack, an old friend who once saved your life, and the smart, handsome partner of your dreams. There can only be one passenger in your car. What is the best strategy? Give the car keys to my old friend and let him take the lady to the hospital; stay behind and wait for the bus with the partner of your dreams.
• The Zorganian Republic has some very strange customs. Couples only wish to have female children as only females can inherit the family's wealth, so if they have a male child they keep having more children until they have a girl. If they have a girl, they stop having children. What is the ratio of girls to boys in Zorgania? (Nice, because "a random string ending in a girl" is the wrong model! It's a string of boys, plus a girl. The right model is a random string, segmented to start with a boy and end with a girl.)
• Focus on one card ... 9/7/8 ... your card has been removed.
• In many London Underground tube stations there are two up escalators but only one going down. Why? People leave trains in a group, so all arrive at the escalators at the same time, but tend to go down to the trains in a more even flow, hence you need less down escalators.
• The amount of water flowing into a tank doubles every minute. The tank is full in an hour. When was the tank half full?
• There are three boxes, one contains only apples, one contains only oranges, and one contains both apples and oranges. The boxes have been incorrectly labeled such that no label identifies the actual contents of the box it labels. Opening just one box, and without looking in the box, you take out one piece of fruit. By looking at the fruit, how can you immediately label all of the boxes correctly? Open the box that is labeled "Apples and Oranges". You know that since none of the labels are correct, the box must either contain only apples, or only oranges.Suppose that you remove an apple from that box. Therefore, that box must be the "Apples Only" box.One of the two remaining boxes must be the "Oranges Only" box. However, one is labeled "Apples Only", and the other is labeled "Oranges Only". Therefore, the one labeled "Apples Only" is the box that contains only oranges, and the box labeled "Oranges Only" is the box that contains both kinds of fruit.
• A boy and a girl are sitting on the porch. "I'm a boy," says the child with black hair. "I'm a girl," says the child with red hair. If at least one of them is lying, who is which?
• You have a 10-gallon jug and a 3-gallon jug. Neither jug is labeled. You need exactly 5 gallons of water. You have a working water faucet right next to you. How can you get exactly 5 gallons of water?
• You are in the dark, and on the floor there are six shoes of three colors, and a heap of twenty-four socks, which are either black or brown. How many socks and shoes must you take into the light to be certain that you have a matching pair of socks and a matching pair of shoes?
• There are 27 gold coins. All of them are fake except for one. All of them appear exactly the same, and there is no way to tell them apart - except that the real gold coin is slightly heavier than the others. Using a balance scale, how can you determine which is the fake coin, with only three weighings?
• Janice and Marge were roommates in college, and meet again after many years. What are the ages of each of the children? Here is their discussion:

Janice: I have three children.

Marge: That's nice! How old are they?

Janice: Well, the product of their ages is 36.

Marge: Ah - I need more information.

Janice: The sum of their ages is the number of coins I have in my wallet.

Marge: That’s still not enough information.

Janice: The oldest one has blue eyes.

Marge: Now I know their ages!

• How can you arrange 6 identical pencils in such as way as to form 4 identical triangles whose sides area are all equal, without modifying the pencils in any way?
• Divide an L-shaped plot into four equal parts.
• Someone did a survey to see how many siblings people had. He carried out his statistical research by stopping people at random in the street and asking them how many brothers and sister they had. To his surprise he found that the average number of siblings people had on the street were much higher than the average from a door to door household survey. Unfortunately he hadn't realised that large families are disproportionately over represented on the streets as each family has more siblings out and about.
• A blind man is all alone in a mountain hut. He has to take two different pills before nightfall today and tomorrow - the pills are identical in shape, weight and size, but one is red and the other one blue. He has two pills of each. But unfortunately he drops them on the floor. While he manages to find all four, they are now all jumbled up. And if he takes two of the same type by accident, he will overdose and die. What should he do?

Questions used

A farmer goes to the village pub after a hard day's work and takes his dog along. The village is two kilometres away, and the farmer walks at a leisurely 4 km per hour. The dog is impatient to get out, it knows the way well and it runs ahead to the pub at a constant speed of 8 km per hour. When the dog arrives, it turns around and runs back until it meets the farmer, then takes off again to the pub, back to the farmer, to the pub, and so on until they both arrive. "Good dog!" says the farmer and gets a few bones for the dog from the innkeeper.

How far in total did the dog run? [I don't know...]

Seriously?
Have you thought about this for more than 5 minutes?
Or did you perhaps try to add up the path segments for the dog and get confused?
Maybe you need a hint ... [Ok. A hint please...]

I wouldn't bother adding up the dog's path segments. Perhaps you can take a more global view. [No. I still don't get it...]

It takes the farmer half an hour to reach the inn. The dog runs all this time at a speed of 8 km per hour. So the dog runs a total of 4 kilometres, regardless of the path it takes.

You go to the Toronto Zoo. You see giraffes, ostriches and a green tree python. Altogether they have 30 eyes and 44 legs.

How many necks does this group of animals have? [I don't know...]

Seriously?
This may be easier than you think.
Maybe you are wondering whether snakes have necks? (TLDR; It's complicated. But: yes.)
Or do you need a hint? [Ok. A hint please...]

Maybe you are just confused by some irrelevant information.[No. I still don't get it...]

It's really quite simple. Thirty eyes are in fifteen heads. Fifteen heads are attached to fifteen necks. Fifteeeen. No more. No less.
How many of each? You could calculate this by substitution. Eight giraffes. Six ostriches. And one snake. But that wasn't the question.

In many London Underground tube stations there are two escalators going up but only one going down.

Why? [I don't know...]

Seriously?
Could it have something to do with the required capacity?
Then just model the expected flow. Is it symmetric?
If you think so, you might need a hint... [Ok. A hint please...]

When do people arrive at the escalator?[Sorry. I still don't get it: aren't there as many going down as coming up?]

We'll we'd hope that the number of people going down is the same as coming up. If there were twice as many people coming up, they must have been produced in the underground - an army of tube zombies, bred in the tunnels, spreading through town to do their evil deeds...
No: the answer has to do with how the streams of passengers distribute over time. Passengers trickle into the station at more or less a constant rate, but when a train arrives, there's a mad scramble by an impatient horde to exit the station, and for that rush the escalators need greater capacity.

Sometimes it is easy to identify gender from names, especially if the name is taken from a religious tradition. Abraham comes to mind, or Eve. So you read a novel where one sunny day, in a schoolyard, Abraham is looking at Pat, and Pat is looking at Eve.

Can you (reasonably) know if a boy is looking at a girl? [I don't know... I mean I don't know the answer ...]

Seriously?
You're probably uncertain about Pat: Patrick? Patricia?
Hm. Do you need a hint... [Ok. A hint please...]

Does it matter?[Sorry. Of course it matters whether Pat is a girl or a boy - how could it not?]

If you think it matters, you're both right and wrong. You're right in the sense that it makes a difference. But you're wrong that it matters for the answer: if Pat is a girl, the boy Abraham looks at a girl. But if Pat is a boy, then he is looking at the girl Eve. So the answer is: yes, you can reasonably know that a boy is looking at a girl. Often, you just need to enumerate all possibilities...

Now: why "reasonably"? Well, I can't exclude that some parents named their daughter Abraham, or that they were confused about Eve ... but hey, it's just a puzzle.

Utilities

PediaPress mwlib mediaWiki → eBook extension/software.

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biochemistry.utoronto.ca/steipe/abc/376CEB52AF96EA94