BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

Contains fulltext : 70137.pdf ( ) (Open Access)BACKGROUND: In many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and differences between the data sets they are analyzing. One of the most popular methods to visualize the overlap and differences between data sets is the Venn diagram: a diagram consisting of two or more circles in which each circle corresponds to a data set, and the overlap between the circles corresponds to the overlap between the data sets. Venn diagrams are especially useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond to the sizes of the data sets. Currently there are no programs available that can create area-proportional Venn diagrams connected to a wide range of biological databases. RESULTS: We designed a web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area-proportional Venn diagrams. The user only needs to input these lists of identifiers in the textboxes and push the submit button. Parameters like colors and text size can be adjusted easily through the web interface. The position of the text can be adjusted by 'drag-and-drop' principle. The output Venn diagram can be shown as an SVG or PNG image embedded in the web application, or as a standalone SVG or PNG image. The latter option is useful for batch queries. Besides the Venn diagram, BioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. Finally, BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes. CONCLUSION: BioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.cmbi.ru.nl/cdd/biovenn/

Applying a Realist Evaluation approach to identify key considerations that successfully enables expansion of Project LEO

Thesis (MPA)--Stellenbosch University, 2022.AFRIKAANSE OPSOMMING: Innovasie en tegnologie is die dryfkrag agter die sakewêreld, die samelewing en die manier waarop ons werk, en die wêreld bly al vinniger verander. Demokratiese beginsels, billikheid, gelykheid en volhoubaarheid is reeds globale kwessies wat in regerings, besighede en die burgerlike samelewing se beste belang is om die hoof te bied. Hierdie maatskaplike kwessies is gesetel in komplekse kontekste met sosio-ekonomiese, politieke, tegnologiese, omgewings- en kulturele faktore wat in berekening gebring en genavigeer moet word. Die regering is toenemend bereid om met die openbare sektor saam te werk om maatskaplike kwessies aan te pak, met behulp van ʼn netwerkbenadering tot bestuursbeheer om die koste van verandering en innovasie te deel, terwyl maatskaplike rolspelers bemagtig word om verandering aan te dryf. Loodsstudies is fundamenteel tot die konseptualisering en toets van veranderingsmeganismes en innoverende intervensies, deurdat verandering in mikrosamelewings bestuur kan word, en indien suksesvol, teen ʼn groter of ander agtergrond herhaal kan word. Realistiese evaluasies gee toe dat nie alle programme dieselfde in verskillende kontekste werk nie en ondersoek eerder wat, vir wie en in watter omgewing werk. Hierdie navorsingsverslag hersien, met behulp van realistiese-evaluasieteorie, die hoofoorwegings vir innoverende loodsstudies wat herhaalbaar is en waar die suksesvolle projekte uitgebrei kan word. Die energiebedryf word gekonfronteer deur die uitdagings van ontkoling en die infrastruktuurveranderinge wat nodig is om die groen revolusie te ondersteun. Hierdie navorsing gee ʼn oorsig oor die kompleksiteit van hierdie oorgang, en ontleed die dryfkragte, rolspelers en beleide wat kompleksiteit in die omgewing veroorsaak. Die Local Energy Oxfordshire (LEO) projek word as ʼn gevallestudie in die navorsing gebruik. Die LEO is ʼn uitstekende voorbeeld van ʼn innoverende loodsprojek, wat verandering in die energiebedryf aandryf deur aanpasbare plaaslike energiestelsels te skep. Die LEO is in Oxfordshire in die Verenigde Koninkryk geloods en, as dit suksesvol is, sal dit dalk nasionaal en in ander lande geïmplementeer word. Die navorsing gebruik realistiese-evalueringsteorie om vroeë aanduiders van sukses te ontleed deur te probeer verstaan of die uitdagings en sukses wat geïdentifiseer word, intern of ekstern tot die omgewing is. Hierdie benadering beoordeel of die intervensie op makroskaal herhaalbaar sal wees, met die inkorporasie van kompleksiteitsteorie aan die kern daarvan. Empiriese navorsing, ingewin deur realistiese onderhoude, bevind dat die LEO vroeë aanduiders van sukses toon, ná holistiese assessering van die maatskaplike kwessies binne die energiesektors wat met hernubare energieverbruik verband hou. Die LEO het verskeie kundige leweringsvennote met diverse netwerke wat maatskaplike hulpbronne kan mobiliseer. Die LEO het ook ʼn bloudruk vir hulle metodologieë, projekontwerpe en implementeringsmetodes ontwikkel, wat deur leweringsdryfkragte in alternatiewe omstandighede aangewend en toegepas kan word. Desondanks sal daar uitdagings met die vergroting van skaal wees, waaronder die toewyding van belanghebbendes aan die bereiking van uitkomste, politieke en gemeenskapsteun, netwerkkundigheid, en betrekkinge met belanghebbendes wat as die interne faktore van die bedryfsomgewing beskou word. Aanbevelings is gedoen om hierdie projekuitdagings die hoof te bied, en daar is ook aanbeveel dat ander loodsstudies gedoen word om innovasie en verandering in alternatiewe omgewings te toets.ENGLISH SUMMARY: Innovation and technology drive business, society and the way in which we work, with the world constantly changing at an increasing rate. Democratic principles, fairness, equality and sustainability have become global issues that governments, businesses and civil society have become invested in addressing. However, these societal issues operate in complex contexts with socio-economic, political, technological, environmental and cultural factors to take into account and navigate. Government has increasingly shown a willingness to work with the public sector to address societal issues, using a network governance approach to share the cost of change and innovation, while empowering social actors to be drivers of change. Pilot studies are fundamental in conceptualising and testing change mechanisms and innovative interventions whereby change is managed in microsocieties and, upon their success, replicated in larger or different settings. Realist evaluations recognise that not all programmes work the same in different contexts and instead investigate what works, for whom and in what environment. Using realist evaluation theory, this research paper reviews the key considerations for innovative pilot studies in realising their aims to achieve replicability and to scale up successful projects. The energy industry faces the challenges of decarbonisation and infrastructural changes required to support the green revolution. This research reviews the complexity of this transition, analysing the driving factors, role players and policies that go towards creating complexity in the environment. Project Local Energy Oxfordshire (LEO) is used as a case study in the research. LEO is a stellar example of an innovative pilot project, driving change in the energy industry by creating flexible local energy systems. LEO is piloted in Oxfordshire, United Kingdom, and if successful, looks to be implemented nationally and in other countries. The research uses realist evaluative theory to analyse early indicators of success by seeking to understand whether challenges and success identified are internal or external to the environment. This approach assesses if the intervention would be replicable at a macro scale, incorporating complexity theory at the core of its operation. The empirical research seen in the format of realist interviews, found that LEO provides early indicators for success, having holistically assessed the societal issues within the energy sectors relating to renewable energy consumption. LEO has a range of committed expert delivery partners, with diverse sets of networks used to mobilise societal resources. Furthermore, LEO has created a blueprint for their piloted methodologies, project designs and implementation methods, which can be utilised and applied by delivery drivers in alternative settings. Despite this, challenges would be faced in scaling up, with stakeholder commitment to achieve outcomes; political and community support; network expertise and stakeholder relationships seen as internal factors of the operating environment. Recommendations have been made to address such project challenges, as well as recommendations for other pilot studies to test innovation and change in alternative environments.Master

Applying a Realist Evaluation approach to identify key considerations that successfully enables expansion of Project LEO

School of Public Leadershi

Benchmarking ortholog identification methods using functional genomics data

BACKGROUND: The transfer of functional annotations from model organism proteins to human proteins is one of the main applications of comparative genomics. Various methods are used to analyze cross-species orthologous relationships according to an operational definition of orthology. Often the definition of orthology is incorrectly interpreted as a prediction of proteins that are functionally equivalent across species, while in fact it only defines the existence of a common ancestor for a gene in different species. However, it has been demonstrated that orthologs often reveal significant functional similarity. Therefore, the quality of the orthology prediction is an important factor in the transfer of functional annotations (and other related information). To identify protein pairs with the highest possible functional similarity, it is important to qualify ortholog identification methods. RESULTS: To measure the similarity in function of proteins from different species we used functional genomics data, such as expression data and protein interaction data. We tested several of the most popular ortholog identification methods. In general, we observed a sensitivity/selectivity trade-off: the functional similarity scores per orthologous pair of sequences become higher when the number of proteins included in the ortholog groups decreases. CONCLUSION: By combining the sensitivity and the selectivity into an overall score, we show that the InParanoid program is the best ortholog identification method in terms of identifying functionally equivalent proteins

Solvates, salts, and cocrystals : a proposal for a feasible classification system

The design of pharmaceutical cocrystals has initiated widespread debate on the classification of cocrystals. Current attempts to classify multicomponent crystals suffer from ambiguity, which has led to inconsistent definitions for cocrystals and for multicomponent crystals in general. Inspired by the work of Aitipamula et al. (Cryst. Growth Des. 2012, 12, 2147-2152), we present a feasible classification system for all multicomponent crystals. The present classification enables us to analyze and classify multicomponent crystal structures present in the Cambridge Structural Database (CSD). This reveals that all seven classes proposed are relevant in terms of frequency of occurrence. Lists of CSD refcodes for all classes are provided. We identified over 5000 cocrystals in the CSD, as well as over 12 000 crystals with more than two components. This illustrates that the possibilities for alternative drug formulations can be increased significantly by considering more than two components in drug design