NFTest: automated testing of Nextflow pipelines.

MOTIVATION: The ongoing expansion in the volume of biomedical data has contributed to a growing complexity in the tools and technologies used in research with an increased reliance on complex workflows written in orchestration languages such as Nextflow to integrate algorithms into processing pipelines. The growing use of workflows involving various tools and algorithms has led to increased scrutiny of software development practices to avoid errors in individual tools and in the connections between them. RESULTS: To facilitate test-driven development of Nextflow pipelines, we created NFTest, a framework for automated pipeline testing and validation with customizability options for Nextflow features. It is open-source, easy to initialize and use, and customizable to allow for testing of complex workflows with test success configurable through a broad range of assertions. NFTest simplifies the testing burden on developers by automating tests once defined and providing a flexible interface for running tests to validate workflows. This reduces the barrier to rigorous biomedical workflow testing and paves the way toward reducing computational errors in biomedicine. AVAILABILITY AND IMPLEMENTATION: NFTest is an open-source Python framework under the GPLv2 license and is freely available at https://github.com/uclahs-cds/tool-NFTest. The call-sSNV Nextflow pipeline is available at: https://github.com/uclahs-cds/pipeline-call-sSNV.

PipeVal: light-weight extensible tool for file validation.

MOTIVATION: The volume of biomedical data generated each year is growing exponentially as high-throughput molecular, imaging and mHealth technologies expand. This rise in data volume has contributed to an increasing reliance on and demand for computational methods, and consequently to increased attention to software quality and data integrity. RESULTS: To simplify data verification in diverse data-processing pipelines, we created PipeVal, a light-weight, easy-to-use, extensible tool for file validation. It is open-source, easy to integrate with complex workflows, and modularized for extensibility for new file formats. PipeVal can be rapidly inserted into existing methods and pipelines to automatically validate and verify inputs and outputs. This can reduce wasted compute time attributed to file corruption or invalid file paths, and significantly improve the quality of data-intensive software. AVAILABILITY AND IMPLEMENTATION: PipeVal is an open-source Python package under the GPLv2 license and it is freely available at https://github.com/uclahs-cds/package-PipeVal. The docker image is available at: https://github.com/uclahs-cds/package-PipeVal/pkgs/container/pipeval.

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?

Software is vital for the advancement of biology and medicine. Through analysis of usage and impact metrics of software, developers can help determine user and community engagement. These metrics can be used to justify additional funding, encourage additional use, and identify unanticipated use cases. Such analyses can help define improvement areas and assist with managing project resources. However, there are challenges associated with assessing usage and impact, many of which vary widely depending on the type of software being evaluated. These challenges involve issues of distorted, exaggerated, understated, or misleading metrics, as well as ethical and security concerns. More attention to the nuances, challenges, and considerations involved in capturing impact across the diverse spectrum of biological software is needed. Furthermore, some tools may be especially beneficial to a small audience, yet may not have comparatively compelling metrics of high usage. Although some principles are generally applicable, there is not a single perfect metric or approach to effectively evaluate a software tool's impact, as this depends on aspects unique to each tool, how it is used, and how one wishes to evaluate engagement. We propose more broadly applicable guidelines (such as infrastructure that supports the usage of software and the collection of metrics about usage), as well as strategies for various types of software and resources. We also highlight outstanding issues in the field regarding how communities measure or evaluate software impact. To gain a deeper understanding of the issues hindering software evaluations, as well as to determine what appears to be helpful, we performed a survey of participants involved with scientific software projects for the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We also investigated software among this scientific community and others to assess how often infrastructure that supports such evaluations is implemented and how this impacts rates of papers describing usage of the software. We find that although developers recognize the utility of analyzing data related to the impact or usage of their software, they struggle to find the time or funding to support such analyses. We also find that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seem to be associated with increased usage rates. Our findings can help scientific software developers make the most out of the evaluations of their software so that they can more fully benefit from such assessments.

Association of advanced age and cancer history with autoimmune disease in melanoma patients: a cross-sectional study.

BACKGROUND: Immune-related adverse events (irAEs) are a major toxicity of immune checkpoint inhibitors. Studies have reported that pre-existing autoimmunity increases the risk of irAEs, but it remains unknown which clinical factors are linked to auto-immune disorders in cancer patients. This study aimed to evaluate if the prevalence of autoimmune diseases varied by specific cancer history and advanced age. METHODS: Our cross-sectional medical record review consisted of 291,333 patients (age, ≥18 years) treated between 2000 and 2018. Patients were classified into four study groups (melanoma only, non-cutaneous solid cancer only, melanoma and non-cutaneous cancer, and no cancer history). Dependent variable was the presence of ≥1 autoimmune disorders based on 98 conditions using 317 ICD codes. RESULTS: Non-cutaneous cancer, in the absence or presence of melanoma, was associated with a higher prevalence of autoimmunity (16.5, 95% CI 16.1-16.9; 20.0, 95% CI 18.3-21.7, respectively) compared to the rates in patients with melanoma only and those without cancer history (9.3, 95% CI 8.6-10.0; 6.2, 95% CI 6.1-6.3, respectively). Among patients with metastases at initial presentation, those in the melanoma and non-cutaneous cancer group had a prevalence of 24.0% (95% CI 20.1-27.9) compared to 19.1% (95% CI 17.2-21.0) in those without metastases. Multiple logistic regression demonstrated that patients > 75 years exhibited the highest odds of autoimmunity relative to other age groups, with age 18-34 as the referent (OR, 1.78, 95% CI 1.67-1.89). CONCLUSIONS: Among patients with melanoma, the greatest prevalence of autoimmunity occurred with advanced age and a history of non-cutaneous cancer.

Hemilability of the 1,2-Bis(dimethylphosphino)ethane (dmpe) Ligand in Cp*Mo(NO)(κ2-dmpe).

Reaction of Cp*Mo(NO)Cl2 with 1 equiv of 1,2-bis(dimethylphosphino)ethane (dmpe) in THF at ambient temperature forms [Cp*Mo(NO)(Cl)(κ2-dmpe)]Cl (1), which is isolable as an analytically pure yellow powder in 65% yield. Further addition of 2 equiv of Cp2Co to 1 in CH2Cl2 affords dark red Cp*Mo(NO)(κ2-dmpe) (2), which was isolated in 36% yield by recrystallization from Et2O at -30 °C. Reaction of a benzene solution of 2 with an equimolar amount of elemental sulfur results in the immediate production of dark blue (µ-S)[Cp*Mo(NO)(κ1-dmpeS)]2 (3), which is a rare example of a bimetallic transition-metal complex bridged by only a single sulfur atom and involving Mo═S═Mo bonding. In contrast, reaction of 2 with an excess of sulfur in benzene results in the formation of Cp*Mo(NO)(η2-S2)(κ1-dmpeS) (4). Complex 4 can also be formed by the addition of elemental sulfur to 3, thereby indicating that 3 is a precursor to 4. Cp*Mo(NO)(κ2-dmpe) (2) also undergoes interesting transformations when treated with organic bromides. For instance, reaction of 2 with 5 equiv benzyl bromide in THF produces the bimetallic complex (µ-dmpe)[Cp*Mo(NO)Br2]2 (5) and bibenzyl after 4 d at 70 °C probably via radical intermediates. In contrast to its reaction with benzyl bromide, complex 2 forms [Mo(NO)Br2(κ2-dmpe)]2 (6), olefin, alkane, and Cp*H when treated with 5 equiv of 1-bromopropane or 1-bromooctane in THF at 70 °C for 72 h. Interestingly, complex 2 does not display any reactivity with bromobenzene or 1-bromoadamantane even after being heated for several days at 70 °C. All new complexes were characterized by conventional spectroscopic and analytical methods, and the solid-state molecular structures of most of them were established by single-crystal X-ray crystallographic analyses.

Thermal Chemistry of Cp*W(NO)(CH2CMe3)(H)(L) Complexes (L = Lewis Base).

The complexes trans-Cp*W(NO)(CH2CMe3)(H)(L) (Cp* = η5-C5Me5) result from the treatment of Cp*W(NO)(CH2CMe3)2 in n-pentane with H2 (∼1 atm) in the presence of a Lewis base, L. The designation of a particular geometrical isomer as cis or trans indicates the relative positions of the alkyl and hydrido ligands in the base of a four-legged piano-stool molecular structure. The thermal behavior of these complexes is markedly dependent on the nature of L. Some of them can be isolated at ambient temperatures [e.g., L = P(OMe)3, P(OPh)3, or P(OCH2)3CMe]. Others undergo reductive elimination of CMe4 via trans to cis isomerization to generate the 16e reactive intermediates Cp*W(NO)(L). These intermediates can intramolecularly activate a C-H bond of L to form 18e cis complexes that may convert to the thermodynamically more stable trans isomers [e.g., Cp*W(NO)(PPh3) initially forms cis-Cp*W(NO)(H)(κ2-PPh2C6H4) that upon being warmed in n-pentane at 80 °C isomerizes to trans-Cp*W(NO)(H)(κ2-PPh2C6H4)]. Alternatively, the Cp*W(NO)(L) intermediates can effect the intermolecular activation of a substrate R-H to form trans-Cp*W(NO)(R)(H)(L) complexes [e.g., L = P(OMe)3 or P(OCH2)3CMe; R-H = C6H6 or Me4Si] probably via their cis isomers. These latter activations are also accompanied by the formation of some Cp*W(NO)(L)2 disproportionation products. An added complication in the L = P(OMe)3 system is that thermolysis of trans-Cp*W(NO)(CH2CMe3)(H)(P(OMe)3) results in it undergoing an Arbuzov-like rearrangement and being converted mainly into [Cp*W(NO)(Me)(PO(OMe)2)]2, which exists as a mixture of two isomers. All new complexes have been characterized by conventional and spectroscopic methods, and the solid-state molecular structures of most of them have been established by single-crystal X-ray crystallographic analyses.

Synthesis, Characterization, and Some Properties of Cp*W(NO)(H)(η(3)-allyl) Complexes.

Sequential treatment at low temperatures of Cp*W(NO)Cl2 in THF with 1 equiv of a binary magnesium allyl reagent, followed by an excess of LiBH4, affords three new Cp*W(NO)(H)(η(3)-allyl) complexes, namely, Cp*W(NO)(H)(η(3)-CH2CHCMe2) (1), Cp*W(NO)(H)(η(3)-CH2CHCHPh) (2), and Cp*W(NO)(H)(η(3)-CH2CHCHMe) (3). Complexes 1-3 are isolable as air-stable, analytically pure yellow solids in good to moderate yields by chromatography or fractional crystallization. In solutions, complex 1 exists as two coordination isomers in an 83:17 ratio differing with respect to the endo/exo orientation of the allyl ligand. In contrast, complexes 2 and 3 each exist as four coordination isomers, all differing by the orientation of their allyl ligands which can have either an endo or an exo orientation with the phenyl or methyl groups being either proximal or distal to the nitrosyl ligand. A DFT computational analysis using the major isomer of Cp*W(NO)(H)(η(3)-CH2CHCHMe) (3a) as the model complex has revealed that its lowest-energy thermal-decomposition pathway involves the intramolecular isomerization of 3a to the 16e η(2)-alkene complex, Cp*W(NO)(η(2)-CH2═CHCH2Me). Such η(2)-alkene complexes are isolable as their 18e PMe3 adducts when compounds 1-3 are thermolyzed in neat PMe3, the other organometallic products formed during these thermolyses being Cp*W(NO)(PMe3)2 (5) and, occasionally, Cp*W(NO)(H)(η(1)-allyl)(PMe3). All new complexes have been characterized by conventional spectroscopic and analytical methods, and the solid-state molecular structures of most of them have been established by single-crystal X-ray crystallographic analyses.

Maximizing benefits from riparian revegetation efforts: local- and landscape-level determinants of avian response.

With limited financial resources available for habitat restoration, information that ensures and/or accelerates success is needed to economize effort and maximize benefit. In the Central Valley of California USA, riparian habitat has been lost or degraded, contributing to the decline of riparian-associated birds and other wildlife. Active restoration of riparian plant communities in this region has been demonstrated to increase local population sizes and species diversity of landbirds. To evaluate factors related to variation in the rate at which bird abundance increased after restoration, we examined bird abundance as a function of local (restoration design elements) and landscape (proportion of riparian vegetation in the landscape and riparian patch density) metrics at 17 restoration projects within five project areas along the Sacramento River. We developed a priori model sets for seven species of birds and used an information theoretic approach to identify factors associated with the rate at which bird abundance increased after restoration. For six of seven species investigated, the model with the most support contained a variable for the amount of riparian forest in the surrounding landscape. Three of seven bird species were positively correlated with the number of tree species planted and three of seven were positively correlated with the planting densities of particular tree species. Our results indicate that restoration success can be enhanced by selecting sites near existing riparian habitat and planting multiple tree species. Hence, given limited resources, efforts to restore riparian habitat for birds should focus on landscape-scale site selection in areas with high proportions of existing riparian vegetation.