BioJava: an open-source framework for bioinformatics

SUMMARY: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language. AVAILABILITY: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.     

Kudi: A free open-source python library for the analysis of properties along reaction paths

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi     

Tagged library approach to chemical genomics and proteomics

Proteomics and chemical genomics face great challenges in the form of molecular libraries of ever increasing size and diversity requiring rapid screening, coupled with a growing number of target proteins for which complimentary molecular ligands are sought. Proteomics and chemical genomics are at a stage that requires techniques which can dramatically accelerate the discovery process. One technique that has shown great promise in accomplishing this is the tagged library approach. It entails the synthetic inclusion of an internal tag from the beginning of the synthesis. This tag adds another degree of functionality to the molecule, in addition to mere ligation, that eliminates the need for time-consuming steps downstream in the process. The tag's functional possibilities span a variety of uses including internal fluorophores, intrinsic binding motifs that enable compound identification, functionalities that play the major role in the synthesis of the ligand itself, and internal linkers that eliminate the need for lengthy 'tether effect' structure-activity relationship studies.     

SCI-Base: an open-source spinal cord injury animal experimentation database

To capture all pertinent data during spinal cord injury animal experimentation, the authors have designed and implemented a database that is available for use under a public license. Their goals were to record all daily medical care of paraplegic animals, including unexpected complications; to store all injury parameters and/or therapeutic procedures; to track locomotor scores and other measures of functional recovery; to allow planning and management of experiments; and to serve as an externally linkable, SQL-queryable data mining source. Ultimately, the use of databases such as this will allow multiple neurotrauma laboratories to compare animal data through web meta-analysis.     

Comparison of fractionation proteomics for local SWATH library building

For data‐independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data‐dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. The quality and coverage of such a reference library is therefore essential when processing SWATH data. In general, library sizes can be increased by reducing the impact of DDA precursor selection with replicate runs or fractionation. However, these strategies can affect the match between the library and SWATH measurement, and thus larger library sizes do not necessarily correspond to improved SWATH quantification. Here, three fractionation strategies to increase local library size were compared to standard library building using replicate DDA injection: protein SDS‐PAGE fractionation, peptide high‐pH RP‐HPLC fractionation and MS‐acquisition gas phase fractionation. The impact of these libraries on SWATH performance was evaluated in terms of the number of extracted peptides and proteins, the match quality of the peptides and the extraction reproducibility of the transitions. These analyses were conducted using the hydrophilic proteome of differentiating human embryonic stem cells. Our results show that SWATH quantitative results and interpretations are affected by choice of fractionation technique. Data are available via ProteomeXchange with identifier PXD006190.     

Implementation of an AI-assisted fragment-generator in an open-source platform

We recently reported a deep learning model to facilitate fragment library design, which is critical for efficient hit identification. However, our model was implemented in Python. We have now created an implementation in the KNIME graphical pipelining environment which we hope will allow experimentation by users with limited programming knowledge.

We report a deep learning model to facilitate fragment library design, which is critical for efficient hit identification, and an implementation in the KNIME graphical workflow environment which should facilitate a more codeless use.     

SEWAL: an open-source platform for next-generation sequence analysis and visualization

Next-generation DNA sequencing platforms provide exciting new possibilities for in vitro genetic analysis of functional nucleic acids. However, the size of the resulting data sets presents computational and analytical challenges. We present an open-source software package that employs a locality-sensitive hashing algorithm to enumerate all unique sequences in an entire Illumina sequencing run (∼10⁸ sequences). The algorithm results in quasilinear time processing of entire Illumina lanes (∼10⁷ sequences) on a desktop computer in minutes. To facilitate visual analysis of sequencing data, the software produces three-dimensional scatter plots similar in concept to Sewall Wright and John Maynard Smith’s adaptive or fitness landscape. The software also contains functions that are particularly useful for doped selections such as mutation frequency analysis, information content calculation, multivariate statistical functions (including principal component analysis), sequence distance metrics, sequence searches and sequence comparisons across multiple Illumina data sets. Source code, executable files and links to sample data sets are available at http://www.sourceforge.net/projects/sewal.     

Boca: an open-source RDF store for building Semantic Web applications

This article presents the design goals and features of the open-source Boca RDF server in the context of a community of cancer-tumor modeling investigators. Boca supplements the desirable data features of the Semantic Web with important enterprise and application features to power a new generation of Semantic-Web-based applications. The data features enable the integration and retrieval of tremendous quantities of diverse data. The enterprise features promote data integrity, fidelity, provenance and robustness. The application features provide for collaborative applications and dynamic user interfaces.     

PhosphoScore: an open-source phosphorylation site assignment tool for MSn data

Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To this end, we have created PhosphoScore, an open-source assignment program that is compatible with phosphopeptide data from multiple MS levels (MS(n)). The algorithm takes into account both the match quality and normalized intensity of observed spectral peaks compared to a theoretical spectrum. PhosphoScore produced >95% correct MS(2) assignments from known synthetic data, > 98% agreement with an established MS(2) assignment algorithm (Ascore), and >92% agreement with visual inspection of MS(3) and MS(4) spectra.     

PROTEIOS: an open source proteomics initiative

SUMMARY: PROTEIOS is an initiative for the development of a comprehensive open source system for storage, organization, analysis and annotation of proteomics experiments. The PROTEIOS platform is based on commonly acknowledged principles for proteomics data publishing. AVAILABILITY: http://www.proteios.org     

distantia: an open-source toolset to quantify dissimilarity between multivariate ecological time-series

There is a large array of methods to extract knowledge and perform ecological forecasting from ecological time-series. However, in spite of its importance for data-mining, pattern-matching and ecological synthesis, methods to assess their similarity are scarce. We introduce distantia (v1.0.1), an R package providing general toolset to quantify dissimilarity between ecological time-series, independently of their regularity and number of samples. The functions in distantia provide the means to compute dissimilarity scores by time and by shape and assess their significance, evaluate the partial contribution of each variable to dissimilarity, and align or combine sequences by similarity. We evaluate the sensitivity of the dissimilarity metrics implemented in distantia, describe its structure and functionality, and showcase its applications with two examples. Particularly, we evaluate how geographic factors drive the dissimilarity between nine pollen sequences dated to the Last Interglacial, and compare the temporal dynamics of climate and enhanced vegetation index of three stands across the range of the European beech. We expect this package may enhance the capabilities of researchers from different fields to explore dissimilarity patterns between multivariate ecological time-series, and aid in generating and testing new hypotheses on why the temporal dynamics of complex-systems changes over space and time.     

VISDA: an open-source caBIG analytical tool for data clustering and beyond

SUMMARY: VISDA (Visual Statistical Data Analyzer) is a caBIG analytical tool for cluster modeling, visualization and discovery that has met silver-level compatibility under the caBIG initiative. Being statistically principled and visually interfaced, VISDA exploits both hierarchical statistics modeling and human gift for pattern recognition to allow a progressive yet interactive discovery of hidden clusters within high dimensional and complex biomedical datasets. The distinctive features of VISDA are particularly useful for users across the cancer research and broader research communities to analyze complex biological data. AVAILABILITY: http://gforge.nci.nih.gov/projects/visda/     

IJ_Rhizo: an open-source software to measure scanned images of root samples

Background and aims

This paper provides an overview of the measuring capabilities of IJ_Rhizo, an ImageJ macro that measures scanned images of washed root samples. IJ_Rhizo is open-source, platform-independent and offers a simple graphic user interface (GUI) for a main audience of non-programmer scientists. Being open-source based, it is also fully modifiable to accommodate the specific needs of the more computer-literate users. A comparison of IJ_Rhizo’s performance with that of the widely used commercial package WinRHIZO? is discussed.

Methods

We compared IJ_Rhizo’s performance with that of the commercial package WinRHIZO? using two sets of images, one comprising test-line images, the second consisting of images of root samples collected in the field. IJ_Rhizo and WinRHIZO? estimates were compared by means of correlation and regression analysis.

Results

IJ_Rhizo “Kimura” and WinRHIZO? “Tennant” were the length estimates that were best linearly correlated with each other. Correlation between average root diameter estimates was weaker, due to the sensitivity of this parameter to thresholding and filtering of image background noise.

Conclusions

Overall, IJ_Rhizo offers new opportunities for researchers who cannot afford the cost of commercial software packages to carry out automated measurement of scanned images of root samples, without sacrificing accuracy.