SPAdes (software)

SPAdes (St. Petersburg genome assembler) is a genome assembly algorithm which was designed for single cell and multi-cells bacterial data sets. However, it might not be suitable for large genomes projects.

SPAdes works with Ion Torrent, PacBio and Illumina paired-end, mate-pairs and single reads. Recently, SPAdes has been integrated into Galaxy pipelines by Guy Lionel and Philip Mabon.

Background

Studying the genome of single cells will help to track changes that occur in DNA over time or associated with exposure to different conditions. Additionally, many projects such as Human Microbiome Project and antibiotics discovery would greatly benefit from Single-cell sequencing (SCS). SCS has an advantage over sequencing DNA extracted from large number of cells. The problem of averaging out the significant variations between cells can be overcome by using SCS. Experimental and computational technologies are being optimized to allow researchers to sequence single cells. For instance, amplification of DNA extracted from a single cell is one of the experimental challenges. To maximize the accuracy and quality of SCS, a uniform DNA amplification is needed. It was demonstrated that using multiple annealing and looping-based amplification cycles (MALBAC) for DNA amplification generates less biasness compared to polymerase chain reaction (PCR) or multiple displacement amplification (MDA). Furthermore, it has been recognized that the challenges facing SCS are computational rather than experimental. Currently available assembler, such as Velvet, String Graph Assembler (SGA) and EULER-SR, were not designed to handle SCS assembly. Assembly of single cell data is difficult due to non-uniform read coverage, variation in insert length, high levels of sequencing errors and chimeric reads. Therefore, the new algorithmic approach, SPAdes, was designed to address these issues.

Software

Computer software also called a program or simply software is any set of instructions that directs a computer to perform specific tasks or operations. Computer software consists of computer programs, libraries and related non-executable data (such as online documentation or digital media). Computer software is non-tangible, contrasted with computer hardware, which is the physical component of computers. Computer hardware and software require each other and neither can be realistically used without the other.

At the lowest level, executable code consists of machine language instructions specific to an individual processor—typically a central processing unit (CPU). A machine language consists of groups of binary values signifying processor instructions that change the state of the computer from its preceding state. For example, an instruction may change the value stored in a particular storage location in the computer—an effect that is not directly observable to the user. An instruction may also (indirectly) cause something to appear on a display of the computer system—a state change which should be visible to the user. The processor carries out the instructions in the order they are provided, unless it is instructed to "jump" to a different instruction, or interrupted.

Software (novel)

Software is a 1982 cyberpunk science fiction novel written by Rudy Rucker. It won the first Philip K. Dick Award in 1983. The novel is the first book in Rucker's Ware Tetralogy, and was followed by a sequel, Wetware, in 1988.

Plot summary

Software introduces Cobb Anderson as a retired computer scientist who was once tried for treason for figuring out how to give robots artificial intelligence and free will, creating the race of boppers. By 2020, they have created a complex society on the Moon, where the boppers developed because they depend on super-cooled superconducting circuits. In that year, Anderson is a pheezer — a freaky geezer, Rucker's depiction of elderly Baby Boomers — living in poverty in Florida and terrified because he lacks the money to buy a new artificial heart to replace his failing, secondhand one.

As the story begins, Anderson is approached by a robot duplicate of himself who invites him to the Moon to be given immortality. Meanwhile, the series' other main character, Sta-Hi Mooney the 1st — born Stanley Hilary Mooney Jr. — a 25-year-old cab driver and "brainsurfer", is kidnapped by a gang of serial killers known as the Little Kidders who almost eat his brain. When Anderson and Mooney travel to the Moon together at the boppers' expense, they find that these events are closely related: the "immortality" given to Anderson turns out to be having his mind transferred into software via the same brain-destroying technique used by the Little Kidders.

Software (development cooperation)

See also

Further reading