Error:
files list file for package `linux-image-2.6.24-19-generic' is missing final newline
Errors were encountered while processing:
/var/cache/apt/archives/linux-image-2.6.24-19-generic_2.6.24-19.36_i386.deb
Processing was halted because there were too many errors.
E: Sub-process /usr/bin/dpkg returned an error code (1)
Fix:
https://lists.ubuntu.com/archives/ubuntu-users/2007-January/104520.html
# move the info dir containing corrupted data out of the
# way, and create a new 'info' dir
cd /var/lib/dpkg
sudo mv info info.bak
sudo mkdir info
# reinstall the affected package, in my case this was
sudo apt-get --reinstall install libgtk1.2
# this will print lots of warnings about missing list
# files for the dependencies, which is obvious.
# now move the newly generated files in 'info/' to the
# 'info.bak/' directory containing info for all packages
# this will replace the information for the package
# we just installed
sudo mv info/* info.bak/
# and now get things back to where they were
sudo rm -rf info
Wednesday, March 17, 2010
alien stone
i maybe a stone, tough on the inside and out and yet as time goes on, i too crumble a bit at a time, i am just a stone after all ...
feels like an alien too, like you don't belong in this world, probably cuz i've been immersed with too much fantasy, anime, dramas lol.
feels like an alien too, like you don't belong in this world, probably cuz i've been immersed with too much fantasy, anime, dramas lol.
pessimist and optimist
A pessimist sees the difficulty in every opportunity;
an optimist sees the opportunity in every difficulty.
—Sir Winston Churchill
an optimist sees the opportunity in every difficulty.
—Sir Winston Churchill
Tuesday, March 16, 2010
Light and Plant Development
1. (9 marks total) These questions pertain to phytochrome and plant development
(a) (2 marks) What is meant by the “photoreversibility” of phytochrome?
Phytochrome exists in 2 interconvertible forms: Pr and Pfr
Conversion of Pr (inactive form) to Pfr (active form) when red light is applied and the process is reversed when far red light is applied
(b) (3 marks) Indicate and explain 3 events involved in the signal transduction pathway leading to active Pfr upon red light illumination (eg. some of the structural and other changes to phytochrome)
Assembly of phytochrome which is a dimer composed of chromophore pigment + polypeptide
chromophore undergoes cis to trans isomerazation when red light is absorbed
Phy protein also undergoes photoreversible conformational change when light is absorbed, autophosphorylation at the Ser in hinge region to expose the PAS domain repeats that contains nuclear localization signals that directs the active form of Pfr into nucleus (regulates gene expression)
His-kinase-related domain mediates autophosphorylation
small amounts of phytochrome remains in the cytosol which mediates rapid responses
(c) (2 marks) What modifying enzymes subsequently affect the stability or activity of the physiologically active form (Pfr) and how do they act?
When Pfr is autophosphorylated at the Ser in the hinge region, it’s less active and less stable form, so phosphatase PAPP5 dephosphorylates the phytochrome making it fully active and stable
On the other hand, a kinase does the reverse process, it phosporylates Pfr to make Pfr less active and less stable so that it can be degraded by proteasome
(d) (2 marks) Once Pfr is activated indicate some processes at the cellular level that are triggered when Pfr remains in the cytosol (Hint: these are changes that mediate rapid responses, the answer is not changes in gene expression. You can indicate the types of responses that are triggered as part of your answer).
- when Pfr is activated, rapid responses (due to ion fluxes) at the cellular level are triggered which cause relatively rapid turgor changes (cell volume changes – swelling / shrinking), organelle movements, stem elongation in pigweeds and in sun plants as shade avoidance response
At equilibrium:
-Saturating red light
85% Pfr
15% Pr
-Saturating far red light
97% Pr
3% Pfr
functional domains of phytochrome:
1. N-terminal half
- Chromophore-binding bilin lyase domain
- PHY domain – stablizes phytochrome in Pfr form
2. Hinge region
- Separates N- from C-terminus; role in conversion: Pr Pfr (active form)
3. PAS domain repeats
- Mediates dimerization & interactions with downstream effector proteins
- Contains NLS (nuclear localization signals) – when exposed, NLSs direct
active form of phytochrome (Pfr) into nucleus
4. His-kinase-related domain
- Mediates autophosphorylation
- Important for stopping phytochrome responses
fluence = amount of light
Law of Reciprocity (VLFR - very low fluence response & LFR)
- Response can be induced by brief pulses of light, provided that the total
amount of light energy adds up to the required fluence
HIR - high irridiance (fluence rate) response
– Need long exposure to light of high irradiance
– Not photoreversible
– Reciprocity does not apply
• i.e. cannot provide dimmer light for a longer time
• Dependent on fluence rate NOT fluence
- eg. induction of flowering, production of ethylene, enlargement of cotyledons, inhibition of hypocotyl elongation
daylight = more red light
canopy and soil = more far-red light
sun plants exhibit shade avoidance in canopies (shade = far-red light only passes through, leaves filters out red-light) - Stem elongates to lift leaves towards light, so in shade, lots of Far-red light, so Pfr is converted to Pr so there's low Pfr:Ptotal ratio when stem elongates
shade-tolerant plants don't do shade avoidance
high Pfr:Ptotal (lots of light) promotes seed germination, optimal growth conditions
photomorphogenesis - driven by changes in gene expression (eg. MYB, LHCB), slower, long term process, convert etiolated (seedling grown in dark, soil - long hypocotyl, apical hook, no chlorophyll) to de-etiolated
in the dark, it's in inactive form, Pr
when red light is present, it is converted to Pfr
How phytochrome was discovered: seeds germinated when exposed to red-light and inhibited when exposed to far-red light (petri dish with seeds), R/FR/R = germinate, the last one determines
(a) (2 marks) What is meant by the “photoreversibility” of phytochrome?
Phytochrome exists in 2 interconvertible forms: Pr and Pfr
Conversion of Pr (inactive form) to Pfr (active form) when red light is applied and the process is reversed when far red light is applied
(b) (3 marks) Indicate and explain 3 events involved in the signal transduction pathway leading to active Pfr upon red light illumination (eg. some of the structural and other changes to phytochrome)
Assembly of phytochrome which is a dimer composed of chromophore pigment + polypeptide
chromophore undergoes cis to trans isomerazation when red light is absorbed
Phy protein also undergoes photoreversible conformational change when light is absorbed, autophosphorylation at the Ser in hinge region to expose the PAS domain repeats that contains nuclear localization signals that directs the active form of Pfr into nucleus (regulates gene expression)
His-kinase-related domain mediates autophosphorylation
small amounts of phytochrome remains in the cytosol which mediates rapid responses
(c) (2 marks) What modifying enzymes subsequently affect the stability or activity of the physiologically active form (Pfr) and how do they act?
When Pfr is autophosphorylated at the Ser in the hinge region, it’s less active and less stable form, so phosphatase PAPP5 dephosphorylates the phytochrome making it fully active and stable
On the other hand, a kinase does the reverse process, it phosporylates Pfr to make Pfr less active and less stable so that it can be degraded by proteasome
(d) (2 marks) Once Pfr is activated indicate some processes at the cellular level that are triggered when Pfr remains in the cytosol (Hint: these are changes that mediate rapid responses, the answer is not changes in gene expression. You can indicate the types of responses that are triggered as part of your answer).
- when Pfr is activated, rapid responses (due to ion fluxes) at the cellular level are triggered which cause relatively rapid turgor changes (cell volume changes – swelling / shrinking), organelle movements, stem elongation in pigweeds and in sun plants as shade avoidance response
At equilibrium:
-Saturating red light
85% Pfr
15% Pr
-Saturating far red light
97% Pr
3% Pfr
functional domains of phytochrome:
1. N-terminal half
- Chromophore-binding bilin lyase domain
- PHY domain – stablizes phytochrome in Pfr form
2. Hinge region
- Separates N- from C-terminus; role in conversion: Pr Pfr (active form)
3. PAS domain repeats
- Mediates dimerization & interactions with downstream effector proteins
- Contains NLS (nuclear localization signals) – when exposed, NLSs direct
active form of phytochrome (Pfr) into nucleus
4. His-kinase-related domain
- Mediates autophosphorylation
- Important for stopping phytochrome responses
fluence = amount of light
Law of Reciprocity (VLFR - very low fluence response & LFR)
- Response can be induced by brief pulses of light, provided that the total
amount of light energy adds up to the required fluence
HIR - high irridiance (fluence rate) response
– Need long exposure to light of high irradiance
– Not photoreversible
– Reciprocity does not apply
• i.e. cannot provide dimmer light for a longer time
• Dependent on fluence rate NOT fluence
- eg. induction of flowering, production of ethylene, enlargement of cotyledons, inhibition of hypocotyl elongation
daylight = more red light
canopy and soil = more far-red light
sun plants exhibit shade avoidance in canopies (shade = far-red light only passes through, leaves filters out red-light) - Stem elongates to lift leaves towards light, so in shade, lots of Far-red light, so Pfr is converted to Pr so there's low Pfr:Ptotal ratio when stem elongates
shade-tolerant plants don't do shade avoidance
high Pfr:Ptotal (lots of light) promotes seed germination, optimal growth conditions
photomorphogenesis - driven by changes in gene expression (eg. MYB, LHCB), slower, long term process, convert etiolated (seedling grown in dark, soil - long hypocotyl, apical hook, no chlorophyll) to de-etiolated
in the dark, it's in inactive form, Pr
when red light is present, it is converted to Pfr
How phytochrome was discovered: seeds germinated when exposed to red-light and inhibited when exposed to far-red light (petri dish with seeds), R/FR/R = germinate, the last one determines
Galaxy
Galaxy
http://galaxy.psu.edu/
Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more...
$ hg clone http://bitbucket.org/galaxy/galaxy-dist/
Fix this error by using virtualenv
> "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py",
> line 343, in reflecttable
> >> raise
> exceptions.NoSuchTableError(table.name)
> >> NoSuchTableError: migrate_version
http://pypi.python.org/pypi/virtualenv
$ virtualenv --not-site-packages ENV
$ export PATH=$HOME/ENV/bin:$PATH
$ ./run.sh
point your browser to
http://127.0.0.1:8080
http://localhost:8080/
http://galaxy.psu.edu/
Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignemnts, compare genomic annotations, profile metagenomic samples and much much more...
$ hg clone http://bitbucket.org/galaxy/galaxy-dist/
Fix this error by using virtualenv
> "/var/lib/python-support/python2.5/sqlalchemy/databases/sqlite.py",
> line 343, in reflecttable
> >> raise
> exceptions.NoSuchTableError(table.name)
> >> NoSuchTableError: migrate_version
http://pypi.python.org/pypi/virtualenv
$ virtualenv --not-site-packages ENV
$ export PATH=$HOME/ENV/bin:$PATH
$ ./run.sh
point your browser to
http://127.0.0.1:8080
http://localhost:8080/
BIRCH and bioLegato
BIRCH is a resource for molecular biology, consisting of software and databases
Most of the programs and databases of BIRCH have been unified through bioLegato. bioLegato is best thought of as a program that runs other programs. As new programs are added to BIRCH, they appear as menu items in bioLegato. bioLegato takes care of all the "behind the scenes" tasks, such as interconverting file formats, allowing the user to concentrate on the science.
http://home.cc.umanitoba.ca/~psgendb/quickintro/quickintro.html
Most of the programs and databases of BIRCH have been unified through bioLegato. bioLegato is best thought of as a program that runs other programs. As new programs are added to BIRCH, they appear as menu items in bioLegato. bioLegato takes care of all the "behind the scenes" tasks, such as interconverting file formats, allowing the user to concentrate on the science.
http://home.cc.umanitoba.ca/~psgendb/quickintro/quickintro.html
Monday, March 15, 2010
Criminology
http://www.prenhall.com/saferstein/
Criminalistics: An Introduction to Forensic Science, 9/e
Richard Saferstein
Glossary
Algor mortis Postmortem changes that cause a body to lose heat.
Autopsy The medical dissection and examination of a body in order to determine the cause of death.
Expert Witness An individual whom the court determines to possess knowledge relevant to the trial that is not expected of the average layperson.
Livor Mortis The medical condition that occurs after death and results in the settling of blood in areas of the body closest to the ground.
Locard’s Exchange Principle Whenever two objects come into contact with one another, there is exchange of materials between them.
Rigor Mortis The medical condition that occurs after death and results in the stiffening of muscle mass. The rigidity of the body gradually disappears 24 hours after death.
Criminalistics: An Introduction to Forensic Science, 9/e
Richard Saferstein
Glossary
Algor mortis Postmortem changes that cause a body to lose heat.
Autopsy The medical dissection and examination of a body in order to determine the cause of death.
Expert Witness An individual whom the court determines to possess knowledge relevant to the trial that is not expected of the average layperson.
Livor Mortis The medical condition that occurs after death and results in the settling of blood in areas of the body closest to the ground.
Locard’s Exchange Principle Whenever two objects come into contact with one another, there is exchange of materials between them.
Rigor Mortis The medical condition that occurs after death and results in the stiffening of muscle mass. The rigidity of the body gradually disappears 24 hours after death.
Python WSGI web test
Web Test
http://pythonpaste.org/webtest/
Werkzeug
http://werkzeug.pocoo.org/documentation/0.6/test.html
http://pythonpaste.org/webtest/
Werkzeug
http://werkzeug.pocoo.org/documentation/0.6/test.html
Friday, March 12, 2010
LIMS - laboratory information management system
http://en.wikipedia.org/wiki/Laboratory_information_management_system
description logics - dl, alc
Description logics
• Formalisms for expressing concepts, their attributes (or
associated roles), and the relationships between them.
• Can be regarded as providing a KR system based on a
structured representation of knowledge.
Description Logic: (p138) - Ch 9
Three types of non-logical symbols:
• atomic concepts:
Dog, Teenager, GraduateStudent
We include a distinguished concept: Thing
• roles: (all are atomic)
:Age, :Parent, :AreaOfStudy
• constants:
johnSmith, chair128
Four types of logical symbols:
• punctuation: [, ], (, )
• positive integers: 1, 2, 3, ...
• concept-forming operators: ALL, EXISTS, FILLS, AND
• connectives: =, =, and →
[AND Company
For example: [EXISTS 7 :Director]
[ALL :Manager [AND Woman
“a company with at least 7 directors,
whose managers are all women with [FILLS :Degree phD]]]
PhDs, and whose min salary is $24/hr” [FILLS :MinSalary $24.00/hour]]
([AND Surgeon Female] = Doctor) is not valid.
C= is subsumed-by
But it is entailed by a KB that contains
(Surgeon = [AND Specialist [FILLS :Specialty surgery]])
(Specialist C= Doctor)
computing subsumption, that is, determining
whether or not KB = (d subsumed-by e) - 'no negation of alpha query)
assumptions:
- KB is acyclic
- d is atomic, only appears once in LHS
- replace
Under these assumptions, it is sufficient to do the following:
• normalization: using the definitions in the KB, put d and e into a special
normal form, d′ and e′
• structure matching: determine if each part of e′ is matched by a part of d′.
- In other words, for every part of the more general concept,
there must be a corresponding part in the more specific one.
p153. [and person [fills :age 27]
computing satisfaction: To determine if KB = (c → e), we use the following procedure:
1. find the most specific concept d such that KB = (c → d)
2. determine whether or not KB = (d C= e), as before.
joe->person , canCorp, joe is manager of cancorp, manager of cancorp is canadian, so you get joe->canadian
computing classification:
- Positioning a new atom in a taxonomy is called classification
- wine example, Wine is at the top root node, then there's white-very-dry-bordeaux-wine
The Logic ALC
Main components:
• Concepts: classes of individuals
• Roles: binary relations between individuals
• Complex concepts using constructors
• Define terminology: TBox
• Give assertions: ABox
Examples:
• Concept names: Person, Female
• Role names: ParentOf, HasHusband
• Individual names: John, Mary
Assertion C(a) (in B&L it's a->C)
MotherWithoutDaughter = Mother ∀ParentOf.¬Female
(P erson M ale)(John)
A Tableaux Algorithm for ALC (Attributive Concept Language with Complements, more expressive DLs)
• Try to prove concept satisfiability by constructing a model.
• A tableau is a graph representing such a model.
• A set of tableaux expansion rules is used to construct the tableau.
• Either a model is constructed or there is an obvious contradiction.
• If tree T contains a clash the concept C is unsatisfiable.
Unfolded: expand every concept name occurring in C
• Formalisms for expressing concepts, their attributes (or
associated roles), and the relationships between them.
• Can be regarded as providing a KR system based on a
structured representation of knowledge.
Description Logic: (p138) - Ch 9
Three types of non-logical symbols:
• atomic concepts:
Dog, Teenager, GraduateStudent
We include a distinguished concept: Thing
• roles: (all are atomic)
:Age, :Parent, :AreaOfStudy
• constants:
johnSmith, chair128
Four types of logical symbols:
• punctuation: [, ], (, )
• positive integers: 1, 2, 3, ...
• concept-forming operators: ALL, EXISTS, FILLS, AND
• connectives: =, =, and →
[AND Company
For example: [EXISTS 7 :Director]
[ALL :Manager [AND Woman
“a company with at least 7 directors,
whose managers are all women with [FILLS :Degree phD]]]
PhDs, and whose min salary is $24/hr” [FILLS :MinSalary $24.00/hour]]
([AND Surgeon Female] = Doctor) is not valid.
C= is subsumed-by
But it is entailed by a KB that contains
(Surgeon = [AND Specialist [FILLS :Specialty surgery]])
(Specialist C= Doctor)
computing subsumption, that is, determining
whether or not KB = (d subsumed-by e) - 'no negation of alpha query)
assumptions:
- KB is acyclic
- d is atomic, only appears once in LHS
- replace
Under these assumptions, it is sufficient to do the following:
• normalization: using the definitions in the KB, put d and e into a special
normal form, d′ and e′
• structure matching: determine if each part of e′ is matched by a part of d′.
- In other words, for every part of the more general concept,
there must be a corresponding part in the more specific one.
p153. [and person [fills :age 27]
computing satisfaction: To determine if KB = (c → e), we use the following procedure:
1. find the most specific concept d such that KB = (c → d)
2. determine whether or not KB = (d C= e), as before.
joe->person , canCorp, joe is manager of cancorp, manager of cancorp is canadian, so you get joe->canadian
computing classification:
- Positioning a new atom in a taxonomy is called classification
- wine example, Wine is at the top root node, then there's white-very-dry-bordeaux-wine
The Logic ALC
Main components:
• Concepts: classes of individuals
• Roles: binary relations between individuals
• Complex concepts using constructors
• Define terminology: TBox
• Give assertions: ABox
Examples:
• Concept names: Person, Female
• Role names: ParentOf, HasHusband
• Individual names: John, Mary
Assertion C(a) (in B&L it's a->C)
MotherWithoutDaughter = Mother ∀ParentOf.¬Female
(P erson M ale)(John)
A Tableaux Algorithm for ALC (Attributive Concept Language with Complements, more expressive DLs)
• Try to prove concept satisfiability by constructing a model.
• A tableau is a graph representing such a model.
• A set of tableaux expansion rules is used to construct the tableau.
• Either a model is constructed or there is an obvious contradiction.
• If tree T contains a clash the concept C is unsatisfiable.
Unfolded: expand every concept name occurring in C
Thursday, March 11, 2010
Open Data
http://radar.oreilly.com/2010/03/truly-open-data.html
open source practices to making data available to the public
http://agbt.org/about.html
The 11th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 24-27, 2010. The AGBT meeting is now widely regarded as the premier scientific forum for capturing information about the latest advances in new DNA sequencing technologies and their applications to diverse areas in biology and biomedical research. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks.
http://twitter.com/bffo
open source practices to making data available to the public
http://agbt.org/about.html
The 11th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 24-27, 2010. The AGBT meeting is now widely regarded as the premier scientific forum for capturing information about the latest advances in new DNA sequencing technologies and their applications to diverse areas in biology and biomedical research. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks.
http://twitter.com/bffo
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