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OS

Two’s complement: In general, to extend an unsigned number, one makes all the new bits of the expanded number 0.

x86 Real mode (state at boot; 20-bit address, no virtual memory; no paging)

x86 Protected mode (VM, segmentation and paging)

x86 Long mode

Ring 0: os operation mode

cr3 (control register 3) point to current paging table

Page flags: 3 bits for OS to use

TLB (Translation Lookaside Buffer) is not coherent with memory (tlb_invalidate)

To paraphrase Parkinson's law, "Programs expand to fill the memory available to hold them."

English

A leap of faith, in its most commonly used meaning, is the act of believing in or accepting something intangible or unprovable, or without empirical evidence.

His house is an eclectic mixture of the antique and the modern.

An innate knowledge of right and wrong.

Nomenclature is a system of naming things, especially in science.

OS

convert the unsigned word in AX to an unsigned double word in EAX.

movzx eax, ax ; extends ax into eax

Bioinformatics

In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

The Smith-Waterman algorithm is a well-known algorithm for performing local sequence alignment; that is, for determining similar regions between two nucleotide or protein sequences.

Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i.e., DNA, RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis.

Primers, which are short single strands of RNA, are synthesized by a protein complex called primase and latch on to specific positions in the newly opened strands, providing an anchor for the next step.

A DNA polymerase, a molecular machine, binds to each freshly separated template strand of the DNA. DNA helicase separates strands, DNA polymerase ensures proper complementarity of bases.

Proteins form enzymes that perform biochemical reactions, send signals to other cells, form the body's major components, like keratin in our skin.

They worked with the bread mold Neurospora, which can survive by consuming very simple nutrients like sucrose and salt.

OS

Floppy and hard disks for PCs are divided into 512 byte regions called sectors. A sector is the disk's minimum transfer granularity: each read or write operation must be one or more sectors in size and aligned on a sector boundary.

When you compile and link a C program, the compiler transforms each C source ('.c') file into an object ('.o') file containing assembly language instructions encoded in the binary format expected by the hardware. The linker then combines all of the compiled object files into a single binary image, which in this case is a binary in the ELF format, which stands for "Executable and Linkable Format".

Bioinformatics

Chargaff rule describes the adenine-to-thymine and guanine-to-cytosine relationshhip in DNA.

Eukaryotic cells encapsulate their DNA in a nucleus and prokaryotics do not. All multicellular organisms are eukaryotic while most unicellular organisms are prokaryotics.

Enlisth

Our bodies constantly metabolize the food we eat.

The only existing treatment for severe combined immunodeficiency (SCID) is bone marrow transplantation.

Algorithm

Halting Problem cannot be solved by any computer.

Whether a 3-CNF (conjunctive normal form) is satisfiable is NPC.

Stated in a way that has more relevance to NP-completeness, if we can provide evidence that a decision problem is hard, we also provide evidence that its related optimization problem is hard.

English

Riley and Vasarely are two noteable artists who made contributions in the illusory world of op art. A style with graphic abstraction and pattern-oriented optical effects (mid-20th century).

The boxer suffered from many blows in the boxer ring.

Ginseng is a medicine made from the root of a Chinese plant, that some people think keeps you young and healthy.

A period of life characterized by physiological and psychic change that marks the end of the reproductive capacity of women and terminates with the completion of menopause.

Squat is often used in negative sentences for emphasis. He had a job that paid him squat.

The mother was all on edge when her son was having a blood test.

Contrary to Bill Clinton's claim that he never got special favors, his uncle pulled strings and ran a "concerted lobbying campaign" that helped the Democratic presidential candidate dodge the Vietnam draft, the Los Angeles Times reported yesterday.

The other day when I was sitting in my basement with Nate and this female I had to third wheel it.

High seas are the open seas of the world outside the territorial waters of any nation.

OS

interrupts

synchronous: caused by CPU (Divide by zero, System call, Bad pointer derefernce) asynchronous: caused by an external event (device I/0, timer ticks)

Intel nomenclature

Interrupt: asynchronous interrupts Exception: synchronous interrupts

x86 interrupts

interrupts types (0-255):

  • Type 0-31 are for processor interrupts, fixed by intel
  • Type 13 general protection fault (An unauthorized int instruction)
  • Type 14 always for page faults
  • Type 32-255 are software configured
  • Type 32-47 are for device interrupts (IRQ) in JOS
  • Type 0x80 interrupts for system call in Linux
  • Control jump to kernel. Kernel code runs and handles the interrupt.
  • The register state of the program (sometimes extra info in CPU registers E.g., page faults store the address that caused the fault in the cr2 register) is dumped on the kernel's stack.
  • When handler completes, program resume (see iret instr.)

Powershell

netsh int ip set address name="Lan" source=static add=172.16.5.41 \
    mask=255.255.255.0 gateway=172.16.5.254;
netsh int ip set dns name="Lan" static 219.232.48.61;

Misc

host www.google.com
www.google.com is an alias for www.l.google.com.
www.l.google.com has address 64.233.189.104
www.l.google.com has address 64.233.189.147
www.l.google.com has address 64.233.189.99
www.l.google.com has address 64.233.189.103
www.google.com has address 74.125.115.147

Bioinformatics

The four letters of the DNA alphabet are adenine, thymine, guanine, and cytosine.

A gene is a DNA sequence which acts as a template for building a specific protein.

The genome of a bacteria is typically about 1 million base pairs long.

Viruses are simplest organisms which require a living host. Its genome is about 10,000 base pairs long.

The human genome is about 3 billion base pairs long.

The homology between genes in different organisms is a natural consequence of evolution.

PCR stands for polymerase chain reaction.

Gel electrophoresis separates DNA fragments by the lengths of DNA sequence based on their movement speed in electrically charged Gel.