Older blog entries for sness (starting at number 5403)

Psychomotor vigilance task - Wikipedia, the free encyclopedia

Psychomotor vigilance task - Wikipedia, the free encyclopedia: "The psychomotor vigilance task (PVT) is a sustained-attention, reaction-timed task that measures the speed with which subjects respond to a visual stimulus. Research indicates increased sleep debt or sleep deficit correlates with deteriorated alertness, slower problem-solving, declined psycho-motor skills, and increased rate of false responding. The PVT was championed by David F. Dinges and popularized by its ease of scoring, simple metrics, and convergent validity.[1] However, it was shown that motivation can counteract the detrimental effects of sleep loss for up to 36 hours.[2]"

'via Blog this'

Syndicated 2013-04-03 06:16:00 from sness

Evaluation measures of multiple sequen... [J Comput Biol. 2000 Feb-Apr] - PubMed - NCBI

Evaluation measures of multiple sequen... [J Comput Biol. 2000 Feb-Apr] - PubMed - NCBI: "Multiple sequence alignments (MSAs) are frequently used in the study of families of protein sequences or DNA/RNA sequences. They are a fundamental tool for the understanding of the structure, functionality and, ultimately, the evolution of proteins. A new algorithm, the Circular Sum (CS) method, is presented for formally evaluating the quality of an MSA. It is based on the use of a solution to the Traveling Salesman Problem, which identifies a circular tour through an evolutionary tree connecting the sequences in a protein family. "

'via Blog this'

Syndicated 2013-04-02 18:14:00 from sness

Finite automata and string matching

Finite automata and string matching: "The start and accept states are obvious: they are just the 0- and m-character prefixes. So the only thing we need to decide is what the transition table should look like. If we've just seen "...nan", and see another character "x", what state should we go to? Clearly, if x is the next character in the match (here "o"), we should go to the next longer prefix (here "nano"). And clearly, once we've seen a complete match, we just stay in that state. But suppose we see a different character, such as "a"? That means that the string so far looks like "...nana". The longest partial match we could be in is just "na". So from state "nan", we should draw an arrow labeled "a" to state "na". Note that "na" is a prefix of "nano" (so it's a state) and a suffix of "nana" (so it's a partial match consistent with what we've just seen)."

'via Blog this'

Syndicated 2013-04-01 17:23:00 from sness

Finite automata and string matching

Finite automata and string matching: "The KMP algorithm works by turning the pattern it's given into a machine, and then running the machine. The hard part of KMP is finding the machine.

We need some restrictions on what we mean by "program". This is where "deterministic & finite" come from."

'via Blog this'

Syndicated 2013-03-31 19:11:00 from sness

Finite-state machine - Wikipedia, the free encyclopedia

Finite-state machine - Wikipedia, the free encyclopedia: "A finite-state machine (FSM) or finite-state automaton (plural: automata), or simply a state machine, is a mathematical model of computation used to design both computer programs and sequential logic circuits. It is conceived as an abstract machine that can be in one of a finite number of states. The machine is in only one state at a time; the state it is in at any given time is called the current state. It can change from one state to another when initiated by a triggering event or condition; this is called a transition. A particular FSM is defined by a list of its states, and the triggering condition for each transition."

'via Blog this'

Syndicated 2013-03-31 19:06:00 from sness

Tree Reconciliation | iPlant Collaborative Web Portal

Tree Reconciliation | iPlant Collaborative Web Portal: "The primary goal of the Tree Reconciliation Working Group is to develop an infrastructure to perform large species-gene tree reconciliations involving thousands of taxa and thousands of gene families. Such an infrastructure, able to process datasets of this magnitude, will prove indispensable given the pace at which the genomes of the different species are being sequenced. The iPlant Tree Reconciliation platform is composed of three elements: an analytical pipeline, a database and a visualizer."

'via Blog this'

Syndicated 2013-03-31 02:36:00 from sness

Notung 2.6 : Reconciliation

Notung 2.6 : Reconciliation: "Given a gene tree and a species tree (e.g., Fig. 1), Notung-2.6 will determine:
The duplications, conditional duplications, and losses that occurred
Upper and lower bounds on the time of duplication and conditional duplication
The cost (D/L Score) of the tree"

'via Blog this'

Syndicated 2013-03-31 02:36:00 from sness

Bayesian gene/species tree reconciliation and... [Bioinformatics. 2003] - PubMed - NCBI

Bayesian gene/species tree reconciliation and... [Bioinformatics. 2003] - PubMed - NCBI: "MOTIVATION: Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabilistic models have proven to be both more realistic and powerful than parsimony models"

'via Blog this'

Syndicated 2013-03-31 02:36:00 from sness

5394 older entries...

New Advogato Features

New HTML Parser: The long-awaited libxml2 based HTML parser code is live. It needs further work but already handles most markup better than the original parser.

Keep up with the latest Advogato features by reading the Advogato status blog.

If you're a C programmer with some spare time, take a look at the mod_virgule project page and help us with one of the tasks on the ToDo list!