scholarly journals LevioSAM: Fast lift-over of alternate reference alignments

2021 ◽  
Author(s):  
Taher Mun ◽  
Nae-Chyun Chen ◽  
Ben Langmead
Keyword(s):  
Population Genetics ◽  
Coordinate System ◽  
Data Structures ◽  
Succinct Data Structures ◽  
Reference Coordinate System ◽  
Link Type ◽  
A Chain ◽  
Time Required ◽  
Effective Use

AbstractMotivationAs more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.ResultsLevioSAM is a tool for lifting SAM/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM completes in less than 13% the time required by an aligner when both are run with 16 threads.Availabilityhttps://github.com/alshai/[email protected], [email protected]

scholarly journals Pydigree: a python library for manipulation and forward-time simulation and of genetic datasets

2017 ◽  
Author(s):  
James E. Hicks
Keyword(s):  
Population Genetics ◽  
Data Structures ◽  
Genetic Epidemiology ◽  
Genetic Data ◽  
Link Type ◽  
File Formats ◽  
Time Simulation ◽  
Cross Platform ◽  
User Friendly ◽  
Python Package

AbstractThe development of software for working with data from population genetics or genetic epidemiology often requires substantial time spent implementing common procedures. Pydigree is a cross-platform Python 3 library that contains efficient, user friendly implementations for many of these common functions, and support for input from common file formats. Developers can combine the functions and data structures to rapidly implement programs handling genetic data. Pydigree presents a useful environment for development of applications for genetic data or rapid prototyping before reimplementation in a higher-performance language.Pydigree is freely available under an open source license. Stable sources can be found in the Python Package Index at https://pypi.python.org/pypi/pydigree/, and development sources can be downloaded at https://github.com/jameshicks/pydigree/

2.2. Working Group 2: Conceptual Definitions of Reference Coordinate Systems for Earth Dynamics

1975 ◽  
Vol 26 ◽  
pp. 21-26
Keyword(s):  
Coordinate System ◽  
Working Group ◽  
General Character ◽  
Coordinate Systems ◽  
Reference Coordinate System ◽  
Group 2 ◽  
Definition Of ◽  
Earth Dynamics

An ideal definition of a reference coordinate system should meet the following general requirements:1. It should be as conceptually simple as possible, so its philosophy is well understood by the users.2. It should imply as few physical assumptions as possible. Wherever they are necessary, such assumptions should be of a very general character and, in particular, they should not be dependent upon astronomical and geophysical detailed theories.3. It should suggest a materialization that is dynamically stable and is accessible to observations with the required accuracy.

Learning to Control the Program Evolution Process with Cultural Algorithms

1997 ◽  
Vol 5 (2) ◽  
pp. 181-211 ◽  
Author(s):  
Elena Zannoni ◽  
Robert G. Reynolds
Keyword(s):  
Genetic Programming ◽  
Population Level ◽  
Extraction Process ◽  
Cultural Algorithms ◽  
Genetic Operators ◽  
Regression Problem ◽  
Standard Procedures ◽  
Programming Process ◽  
Time Required ◽  
Effective Use

Traditional software engineering dictates the use of modular and structured programming and top-down stepwise refinement techniques that reduce the amount of variability arising in the development process by establishing standard procedures to be followed while writing software. This focusing leads to reduced variability in the resulting products, due to the use of standardized constructs. Genetic programming (GP) performs heuristic search in the space of programs. Programs produced through the GP paradigm emerge as the result of simulated evolution and are built through a bottom-up process, incrementally augmenting their functionality until a satisfactory level of performance is reached. Can we automatically extract knowledge from the GP programming process that can be useful to focus the search and reduce product variability, thus leading to a more effective use of the available resources? An answer to this question is investigated with the aid of cultural algorithms. A new system, cultural algorithms with genetic programming (CAGP), is presented. The system has two levels. The first is the pool of genetic programs (population level), and the second is a knowledge repository (belief set) that is built during the GP run and is used to guide the search process. The microevolution within the population brings about potentially meaningful characteristics of the programs for the achievement of the given task, such as properties exhibited by the best performers in the population. CAGP extracts these features and represents them as the set of the current beliefs. Beliefs correspond to constraints that all the genetic operators and programs must follow. Interaction between the two levels occurs in one direction through the extraction process and, in the other, through the modulation of an individual's program parameters according to which, and how many, of the constraints it follows. CAGP is applied to solve an instance of the symbolic regression problem, in which a function of one variable needs to be discovered. The results of the experiments show an overall improvement on the average performance of CAGP over GP alone and a significant reduction of the complexity of the produced solution. Moreover, the execution time required by CAGP is comparable with the time required by GP alone.

Teaching Tip: Designing Flipped Classrooms to Enhance Learning in the Clinical Skills Laboratory

2021 ◽  
pp. e20210043
Author(s):  
Sarah Baillie ◽  
Annelies Decloedt ◽  
Molly Frendo Londgren
Keyword(s):  
Student Engagement ◽  
Flipped Classroom ◽  
Clinical Skills ◽  
Face To Face ◽  
Use Of Time ◽  
Skills Laboratory ◽  
The Face ◽  
Expected Benefits ◽  
Time Required ◽  
Effective Use

Flipped classroom is an educational technique in which content is delivered online for students to study at their own pace in preparation for in-class learning. Benefits include increased flexibility, enhanced student engagement and satisfaction, and more effective use of time spent during face-to-face teaching. However, the development and implementation of flipped classroom teaching are also associated with challenges, including time required to develop learning materials and getting students to engage with the preparatory work. This teaching tip describes a structured approach to designing and implementing the flipped classroom approach for clinical skills to allow a greater focus on practicing the hands-on skills and the provision of feedback during the laboratory session. First, the rationale for flipping the classroom and the expected benefits should be considered. On a practical level, decisions need to be made about what to include in the flipped component, how it will complement the face-to-face class, and how the resources will be created. In the design phase, adopting a structured template and aligning with established pedagogical principles is helpful. A well-designed flipped classroom motivates learners by including different elements such as quality educational media (e.g., videos), the opportunity to self-assess, and well-defined connections to relevant knowledge and skills. Student engagement with the flipped material can be promoted through different strategies such as clear communication to manage student expectations and adapting the delivery of the face-to-face component. Finally, gathering feedback and evaluating the initiative are important to inform future improvements.

scholarly journals Mathematical Modeling of Open States in Double Stranded DNA Molecule Depending on 2H/1H Ratio

2019 ◽  
Vol 14 (2) ◽  
pp. 612-624 ◽  
Author(s):  
S.S. Dzhimak ◽  
M.I. Drobotenko ◽  
A.A. Basov ◽  
A.A. Svidlov ◽  
M.G. Baryshev
Keyword(s):  
Mathematical Modeling ◽  
Hydrogen Bond ◽  
Deuterium Atom ◽  
Living System ◽  
Dna Molecule ◽  
Dna Base Pair ◽  
A Chain ◽  
Time Required ◽  
Open States ◽  
Bond Disruption

The evaluation results of the possible deuterium atoms effect on the DNA base pair opening are presented in the article. The cause of these processes is the replacement of protium with deuterium atom due to the increase of energy required to break the hydrogen bond. These processes can be studied by method of mathematical modeling, with account of open states between base pairs being the key condition of the adequacy of the mathematical model of the DNA. The experiment data show that the presence of deuterium in a chain of nucleotides can cause - depending on the value of hydrogen bond disruption energy - both increase and decrease in probability of open states occurrence. For example: hydrogen bond disruption energy of 0.358·10-22 n·m, non-zero probability of open states occurrence is observed in case of the absence of deuterium in the molecule, and with hydrogen bond disruption energy of 0.359·10-22 n·m or more such probability equals zero. Also, when one deuterium atom is present in a molecule, non-zero probability is observed even with hydrogen bond disruption energy equal to 0.368·10-22 n·m (i.e. more than 0.358·10-22 n·m). Thus participation of deuterium atoms in the formation of hydrogen bonds of double helixes of a DNA molecule can cause the changes in the time required for transfer of genetic information, which can explain the effect of even minor deviations in deuterium concentration in a medium on metabolic processes in a living system.

scholarly journals Identity and compatibility of reference genome resources

2021 ◽  
Author(s):  
Michał Stolarczyk ◽  
Bingjie Xue ◽  
Nathan C. Sheffield
Keyword(s):  
Coordinate System ◽  
Genome Analysis ◽  
Reference Genome ◽  
Reference Data ◽  
Coordinate Systems ◽  
Link Type ◽  
Novel Approach ◽  
Many Sources ◽  
Parent Child Relationships ◽  
Parent Child

Genome analysis relies on reference data like sequences, feature annotations, and aligner indexes. These data can be found in many versions from many sources, making it challenging to identify and assess compatibility among them. For example, how can you determine which indexes are derived from identical raw sequence files, or which annotations share a compatible coordinate system? Here, we describe a novel approach to establish identity and compatibility of reference genome resources. We approach this with three advances: First, we derive unique identifiers for each resource; second, we record parent-child relationships among resources; and third, we describe recursive identifiers that determine identity as well as compatibility of coordinate systems and sequence names. These advances facilitate portability, reproducibility, and re-use of genome reference data.Availabilityhttps://refgenie.databio.org

Psychopharmacology in Psychiatric Emergencies

1981 ◽  
Vol 10 (3) ◽  
pp. 189-204 ◽  
Author(s):  
Irl Extein
Keyword(s):  
Psychiatric Treatment ◽  
Emergency Setting ◽  
Antipsychotic Medications ◽  
Psychiatric Emergencies ◽  
Medical Disorders ◽  
Steady State Kinetics ◽  
Sedative Hypnotics ◽  
Time Required ◽  
Effective Use ◽  
Severe Anxiety

Pharmacotherapy is crucial to the emergency psychiatric treatment of patients who are out of control in a variety of psychiatric and medical disorders. The time required for the more definitive pharmacological treatment of the major psychiatric syndromes is such that they can at best be only started in the emergency setting. The emergency treatment of patients who are severely agitated, violent, or psychotic is based on the IM administration of antipsychotic medications, such as haloperidol. In conjunction with psychological support this can provide effective, safe, and humane treatment. Sedative-hypnotics, such as diazepam, can be helpful for less severe anxiety states. This article focused on clinical and pharmacokinetic principles of the use of these medications, the understanding of which can help maximize their effective use in emergencies. Topics which are emphasized include sedative, antipsychotic and disinhibiting effects, side effects, absorption after oral and IM administration, and the concepts of steady-state kinetics and the “loading dose.”

Reference coordinate system in design of shoe lasts

2009 ◽  
Vol 1 (sup1) ◽  
pp. 8-10
Author(s):  
Kirill Zamarashkin ◽  
Nikolai Zamarashkin
Keyword(s):  
Coordinate System ◽  
Reference Coordinate System
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