| 1. |
- Lund, Mikael, et al.
(författare)
-
FAUNUS: An object oriented framework for molecular simulation
- 2008
-
Ingår i: Source Code for Biology and Medicine. - : Springer Science and Business Media LLC. - 1751-0473. ; 3
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: We present a C++ class library for Monte Carlo simulation of molecular systems, including proteins in solution. The design is generic and highly modular, enabling multiple developers to easily implement additional features. The statistical mechanical methods are documented by extensive use of code comments that - subsequently - are collected to automatically build a web-based manual. RESULTS: We show how an object oriented design can be used to create an intuitively appealing coding framework for molecular simulation. This is exemplified in a minimalistic C++ program that can calculate protein protonation states. We further discuss performance issues related to high level coding abstraction. CONCLUSION: C++ and the Standard Template Library (STL) provide a high-performance platform for generic molecular modeling. Automatic generation of code documentation from inline comments has proven particularly useful in that no separate manual needs to be maintained.
|
|
| 2. |
- Dublon, Ian
(författare)
-
Superplot3d: an open source GUI tool for 3d trajectory visualisation and elementary processing
- 2013
-
Ingår i: Source Code for Biology and Medicine. - : Springer Science and Business Media LLC. - 1751-0473. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to rapidly visualise these data. Ordinarily, to achieve this the user must either execute 3d plotting functions in a numerical computing environment or manually inspect data in two dimensions, plotting each individual axis. Superplot3d is an open source MATLAB script which takes tab delineated Cartesian data points in the form x,y,z and time and generates an instant visualization of the object’s trajectory in free-rotational three dimensions. Whole trajectories may be instantly presented, allowing for rapid inspection. Executable from the MATLAB command line (or deployable as a compiled standalone application) superplot3d also provides simple GUI controls to obtain rudimentary trajectory information, allow specific visualization of trajectory sections and perform elementary processing. Superplot3d thus provides a framework for non-programmers and programmers alike, to recreate recently acquired 3d object trajectories in rotatable 3d space. It is intended, via the use of a preference driven menu to be flexible and work with output from multiple tracking software systems. Source code and accompanying GUIDE .fig files are provided for deployment and further development.
|
|
| 3. |
- Ortiz Catalan, Max Jair, 1982, et al.
(författare)
-
BioPatRec: A modular research platform for the control of artificial limbs based on pattern recognition algorithms
- 2013
-
Ingår i: Source Code for Biology and Medicine. - : Springer Science and Business Media LLC. - 1751-0473. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Background Processing and pattern recognition of myoelectric signals have been at the core of prosthetic control research in the last decade. Although most studies agree on reporting the accuracy of predicting predefined movements, there is a significant amount of study-dependent variables that make high-resolution inter-study comparison practically impossible. As an effort to provide a common research platform for the development and evaluation of algorithms in prosthetic control, we introduce BioPatRec as open source software. BioPatRec allows a seamless implementation of a variety of algorithms in the fields of 1) Signal processing; 2) Feature selection and extraction; 3) Pattern recognition; and, 4) Real-time control. Furthermore, since the platform is highly modular and customizable, researchers from different fields can seamlessly benchmark their algorithms by applying them in prosthetic control, without necessarily knowing how to obtain and process bioelectric signals, or how to produce and evaluate physically meaningful outputs. Results BioPatRec is demonstrated in this study by the implementation of a relatively new pattern recognition algorithm, namely Regulatory Feedback Networks (RFN). RFN produced comparable results to those of more sophisticated classifiers such as Linear Discriminant Analysis and Multi-Layer Perceptron. BioPatRec is released with these 3 fundamentally different classifiers, as well as all the necessary routines for the myoelectric control of a virtual hand; from data acquisition to real-time evaluations. All the required instructions for use and development are provided in the online project hosting platform, which includes issue tracking and an extensive "wiki". This transparent implementation aims to facilitate collaboration and speed up utilization. Moreover, BioPatRec provides a publicly available repository of myoelectric signals that allow algorithms benchmarking on common data sets. This is particularly useful for researchers lacking of data acquisition hardware, or with limited access to patients. Conclusions BioPatRec has been made openly and freely available with the hope to accelerate, through the community contributions, the development of better algorithms that can potentially improve the patient's quality of life. It is currently used in 3 different continents and by researchers of different disciplines, thus proving to be a useful tool for development and collaboration.
|
|
| 4. |
- Pornputtapong, Natapol, 1981, et al.
(författare)
-
A dedicated database system for handling multi-level data in systems biology
- 2014
-
Ingår i: Source Code for Biology and Medicine. - : Springer Science and Business Media LLC. - 1751-0473. ; 9:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging.Methods: To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase.Results and conclusion: In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.
|
|
| 5. |
|
|
| 6. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
-
A software pipeline for processing and identification of fungal ITS sequences
- 2009
-
Ingår i: Source Code for Biology and Medicine. - 1751-0473. ; 4:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background Fungi from environmental samples are typically identified to species level through DNA sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region for use in BLAST-based similarity searches in the International Nucleotide Sequence Databases. These searches are time-consuming and regularly require a significant amount of manual intervention and complementary analyses. We here present software - in the form of an identification pipeline for large sets of fungal ITS sequences - developed to automate the BLAST process and several additional analysis steps. The performance of the pipeline was evaluated on a dataset of 350 ITS sequences from fungi growing as epiphytes on building material. Results The pipeline was written in Perl and uses a local installation of NCBI-BLAST for the similarity searches of the query sequences. The variable subregion ITS2 of the ITS region is extracted from the sequences and used for additional searches of higher sensitivity. Multiple alignments of each query sequence and its closest matches are computed, and query sequences sharing at least 50 % of their best matches are clustered to facilitate the evaluation of hypothetically conspecific groups. The pipeline proved to speed up the processing, as well as enhance the resolution, of the evaluation dataset considerably, and the fungi were found to belong chiefly to the Ascomycota, with Penicillium and Aspergillus as the two most common genera. The ITS2 was found to indicate a different taxonomic affiliation than did the complete ITS region for 10 % of the query sequences, though this figure is likely to vary with the taxonomic scope of the query sequences. Conclusions The present software readily assigns large sets of fungal query sequences to their respective best matches in the international sequence databases and places them in a larger biological context. The output is highly structured to be easy to process, although it still needs to be inspected and possibly corrected for the impact of the incomplete and sometimes erroneously annotated fungal entries in these databases. The open source pipeline is available for UNIX-type platforms, and updated releases of the target database are made available biweekly. The pipeline is easily modified to operate on other molecular regions and organism groups.
|
|
