Uppsala University is a research university in Uppsala, is the oldest university in Sweden and all of the Nordic countries still in operation, founded in 1477. It ranks among the world's 100 best universities in several high-profile international rankings; the university embraces natural sciences. The university rose to pronounced significance during the rise of Sweden as a great power at the end of the 16th century and was given a relative financial stability with the large donation of King Gustavus Adolphus in the early 17th century. Uppsala has an important historical place in Swedish national culture and for the Swedish establishment: in historiography, literature and music. Many aspects of Swedish academic culture in general, such as the white student cap, originated in Uppsala, it shares some peculiarities, such as the student nation system, with Lund University and the University of Helsinki. Uppsala belongs to the Coimbra Group of European universities and to the Guild of European Research-Intensive Universities.
The university has nine faculties distributed over three "disciplinary domains". It has 2,300 doctoral students, it has a teaching staff of 1,800 out of a total of 6,900 employees. Twenty-eight per cent of the 716 professors at the university are women. Of its turnover of SEK 6.6 billion in 2016, 29% was spent on education at Bachelor's and Master's level, while 70% was spent on research and research programs. Architecturally, Uppsala University has traditionally had a strong presence in Fjärdingen, the neighbourhood around the cathedral on the western side of the River Fyris. Despite some more contemporary building developments further away from the centre, Uppsala's historic centre continues to be dominated by the presence of the university; as with most medieval universities, Uppsala University grew out of an ecclesiastical center. The archbishopric of Uppsala had been one of the most important sees in Sweden proper since Christianity first spread to this region in the ninth century. Uppsala had long been a hub for regional trade, had contained settlements dating back into the deep Middle Ages.
As was the case with most medieval universities, Uppsala had been chartered through a papal bull. Uppsala's bull, which granted the university its corporate rights, was issued by Pope Sixtus IV in 1477, established a number of provisions. Among the most important of these was that the university was given the same freedoms and privileges as the University of Bologna; this included the right to establish the four traditional faculties of theology, law and philosophy, to award the bachelor's, master's, doctoral degrees. The archbishop of Uppsala was named as the university's Chancellor, was charged with maintaining the rights and privileges of the university and its members; the turbulent period of the reformation of King Gustavus Vasa resulted in a drop in the relatively insignificant number of students in Uppsala, seen as a center of Catholicism and of potential disloyalty to the Crown. Swedish students travelled to one of the Protestant universities in Germany Wittenberg. There is some evidence of academic studies in Uppsala during the 16th century.
At the end of the century the situation had changed, Uppsala became a bastion of Lutheranism, which Duke Charles, the third of the sons of Gustavus Vasa to become king used to consolidate his power and oust his nephew Sigismund from the throne. The Meeting of Uppsala in 1593 established Lutheran orthodoxy in Sweden, Charles and the Council of state gave new privileges to the university on 1 August of the same year. Theology still had precedence, but in the privileges of 1593, the importance of a university to educate secular servants of the state was emphasized. Three of the seven professorial chairs which were established were in Theology. A fourth chair was given to Ericus Jacobi Skinnerus, appointed rector, but whose discipline was not mentioned in the charter. Of the professors, several were taken over from the Collegium Regium in Stockholm, functioning for a few years but closed in 1593. An eighth chair, in Medicine, received no appointee for several years. In 1599 the number of students was 150.
In 1600 the first post-reformation conferment of degrees took place. In the same year, the antiquarian and mystic Johannes Bureus designed and engraved the seal of the university, today used as part of the logotype; the medieval university had been a school for theology. The aspirations of the emergent new great power of Sweden demanded a different kind of learning. Sweden both grew through conquests and went through a complete overhaul of its administrative structure, it required a much larger class of civil educators than before. Preparatory schools, were founded during this period in various cathedral towns, notably Västerås in 1623. Beside Uppsala, new universities were founded in more distant parts of the Swedish Realm, the University of Dorpat in Estonia and the University of Åbo in Finland. Af
In computing, a plug-in is a software component that adds a specific feature to an existing computer program. When a program supports plug-ins, it enables customization. Web browsers have allowed executables as plug-ins, though they are now deprecated. Two plug-in examples are the Adobe Flash Player for playing videos and a Java virtual machine for running applets. A theme or skin is a preset package containing additional or changed graphical appearance details, achieved by the use of a graphical user interface that can be applied to specific software and websites to suit the purpose, topic, or tastes of different users to customize the look and feel of a piece of computer software or an operating system front-end GUI. Applications support plug-ins for many reasons; some of the main reasons include: to enable third-party developers to create abilities which extend an application to support adding new features to reduce the size of an application to separate source code from an application because of incompatible software licenses.
Types of applications and why they use plug-ins: Audio editors use plug-ins to generate, process or analyze sound. Ardour and Audacity are examples of such editors. Digital audio workstations use plug-ins to process it. Examples include ProTools. Email clients use plug-ins to encrypt email. Pretty Good Privacy is an example of such plug-ins. Video game console emulators use plug-ins to modularize the separate subsystems of the devices they seek to emulate. For example, the PCSX2 emulator makes use of video, optical, etc. plug-ins for those respective components of the PlayStation 2. Graphics software use plug-ins to support file formats and process images. Media players use plug-ins to apply filters. Foobar2000, GStreamer, Quintessential, VST, Winamp, XMMS are examples of such media players. Packet sniffers use plug-ins to decode packet formats. OmniPeek is an example of such packet sniffers. Remote sensing applications use plug-ins to process data from different sensor types. Text editors and Integrated development environments use plug-ins to support programming languages or enhance development process e.g. Visual Studio, RAD Studio, IntelliJ IDEA, jEdit and MonoDevelop support plug-ins.
Visual Studio itself can be plugged into other applications via Visual Studio Tools for Office and Visual Studio Tools for Applications. Web browsers have used executables as plug-ins, though they are now deprecated. Examples include Java SE, QuickTime, Microsoft Silverlight and Unity; the host application provides services which the plug-in can use, including a way for plug-ins to register themselves with the host application and a protocol for the exchange of data with plug-ins. Plug-ins depend on the services provided by the host application and do not work by themselves. Conversely, the host application operates independently of the plug-ins, making it possible for end-users to add and update plug-ins dynamically without needing to make changes to the host application. Programmers implement plug-in functionality using shared libraries, which get dynamically loaded at run time, installed in a place prescribed by the host application. HyperCard supported a similar facility, but more included the plug-in code in the HyperCard documents themselves.
Thus the HyperCard stack became a self-contained application in its own right, distributable as a single entity that end-users could run without the need for additional installation-steps. Programs may implement plugins by loading a directory of simple script files written in a scripting language like Python or Lua. In Mozilla Foundation definitions, the words "add-on", "extension" and "plug-in" are not synonyms. "Add-on" can refer to anything. Extensions comprise a subtype, albeit the most powerful one. Mozilla applications come with integrated add-on managers that, similar to package managers, install and manage extensions; the term, "Plug-in", however refers to NPAPI-based web content renderers. Plug-ins are being deprecated. Plug-ins appeared as early as the mid 1970s, when the EDT text editor running on the Unisys VS/9 operating system using the UNIVAC Series 90 mainframe computers provided the ability to run a program from the editor and to allow such a program to access the editor buffer, thus allowing an external program to access an edit session in memory.
The plug-in program could make calls to the editor to have it perform text-editing services upon the buffer that the editor shared with the plug-in. The Waterloo Fortran compiler used this feature to allow interactive compilation of Fortran programs edited by EDT. Early PC software applications to incorporate plug-in functionality included HyperCard and QuarkXPress on the Macintosh, both released in 1987. In 1988, Silicon Beach Software included plug-in functionality in Digital Darkroom and SuperPaint, Ed Bomke coined the term plug-in. Applet Browser extension
Peter Murray-Rust is a chemist working at the University of Cambridge. As well as his work in chemistry, Murray-Rust is known for his support of open access and open data, he was educated at Balliol College, Oxford. After obtaining a Doctor of Philosophy with a thesis entitled A structural investigation of some compounds showing charge-transfer properties, he became lecturer in chemistry at the University of Stirling and was first warden of Andrew Stewart Hall of Residence. In 1982, he moved to Glaxo Group Research at Greenford to head Molecular Graphics, Computational Chemistry and protein structure determination, he was Professor of Pharmacy in the University of Nottingham from 1996–2000, setting up the Virtual School of Molecular Sciences. He is now Reader Emeritus in Molecular Informatics at the University of Cambridge and Senior Research Fellow Emeritus of Churchill College, Cambridge, his research interests have involved the automated analysis of data in scientific publications, creation of virtual communities, e.g.
The Virtual School of Natural Sciences in the Globewide Network Academy, the Semantic Web. With Henry Rzepa, he has extended this to chemistry through the development of markup languages Chemical Markup Language, he campaigns for open data in science, is on the advisory board of the Open Knowledge International and a co-author of the Panton Principles for Open scientific data. Together with a few other chemists, he was a founder member of the Blue Obelisk movement in 2005. In 2002, Peter Murray-Rust and his colleagues proposed an electronic repository for unpublished chemical data called the World Wide Molecular Matrix. In January 2011, a symposium around his career and visions was organized, called Visions of a Semantic Molecular Future. In 2011, he and Henry Rzepa were joint recipients of the Herman Skolnik Award of the American Chemical Society. In 2014, he was awarded a Fellowship by the Shuttleworth Foundation to develop the automated mining of science from the literature. In 2009 Murray-Rust coined the term "Doctor Who" model for the phenomenon exhibited by the Blue Obelisk project and other Open Science projects, where when a project leader does not have the resources to continue to lead a project, someone else will stand up to become the new leader and continue the project.
This is a reference to the long-running British science fiction television series Doctor Who, in which the main character periodically regenerates into a different form, played by a different actor. As of 2014, Murray-Rust was granted a Fellowship by Shuttleworth Foundation in relation to the ContentMine project which uses machines to liberate 100,000,000 facts from the scientific literature. Murray-Rust is known for his work on making scientific knowledge from literature available, in such taking a stance against publishers that are not compliant with the Berlin Declaration on Open Access. In 2014, he raised awareness of glitches in the publishing system of Elsevier, where restrictions were imposed by Elsevier on the reuse of papers after the authors had paid Elsevier to make the paper available, he has made statements about predatory journals. Cambridge university page Peter Murray-Rust on Twitter Doctoral thesis, "A structural investigation of some compounds showing charge-transfer properties"
European Bioinformatics Institute
The European Bioinformatics Institute is an IGO which as part of the European Molecular Biology Laboratory family focuses on research and services in bioinformatics. The roots of the EMBL-EBI lie in the EMBL Nucleotide Sequence Data Library, established in 1980 at the EMBL laboratories in Heidelberg and was the world's first nucleotide sequence database; the original goal was to establish a central computer database of DNA sequences, to supplement sequences submitted to journals. What began as a modest task of abstracting information from literature soon became a major database activity with direct electronic submissions of data and the need for skilled informatics staff; the task grew in scale with the start of the genome projects, grew in visibility as the data became relevant to research in the commercial sector. It soon became apparent that the EMBL Nucleotide Sequence Data Library needed better financial security to ensure its long-term viability and to cope with the sheer scale of the task.
There was a need for research and development to provide services, to collaborate with global partners to support the project, to provide assistance to industry. To this end, in 1992, the EMBL Council voted to establish the European Bioinformatics Institute and to locate it at the Wellcome Trust Genome Campus in the United Kingdom where it would be in close proximity to the major sequencing efforts at the Wellcome Sanger Institute. From 1992 through to 1994, a gradual transition of the activities in Heidelberg took place, until in September 1994 the EMBL-EBI occupied its current location on the Wellcome Trust Genome Campus; when the EMBL-EBI moved to Hinxton it hosted two databases, one for nucleotide sequences and one for protein sequences. Since the EMBL-EBI has diversified to provide data resources in all the major molecular domains and expanded to include a broad research base, it offers advanced training in bioinformatics. Since 2013, EMBL-EBI has been listed as a data and service provider in the Registry of Research Data Repositories.
As part of EMBL, the largest part of EMBL-EBI's funding comes from the governments of EMBL's 21 member states. Other major funders include the European Commission, Wellcome Trust, US National Institutes of Health, UK Research Councils, EMBL-EBI's industry partners and the UK Department for Business and Skills. In addition, the Wellcome Trust provides the facilities for the EMBL-EBI on its Genome Campus at Hinxton, the UK Research Councils have provided funds for EMBL-EBI's facilities in Hinxton; the EMBL-EBI hosts a number of publicly open, free to use life science resources, including biomedical databases, analysis tools and bio-ontologies. These include: ArrayExpress – archive of gene expression experiments BioModels – a database of computational models relevant to the life sciences BioStudies – a database that serves as a generic data archive at EMBL-EBI for biomolecular datasets Chemical Entities of Biological Interest – database and ontology of molecular entities European Nucleotide Archive – resource of nucleotide sequencing information Ensembl project – genome databases for vertebrates and other eukaryotic species Europe PubMed Central – database offering free access to collection of biomedical research literature Experimental Factor Ontology – ontology of experimental variables for biomedical data Expression Atlas – database of summary information on which genes are expressed under which conditions Gene ontology – ontology of gene functions and processes InterPro – database of protein functional domains and families MetaboLights – repository of metabolomics data Protein Data Bank in Europe – European resource for the collection and dissemination of data on biological macromolecular structures Proteomics Identifications Database – repository of mass spectrometry based proteomics UniProt – database of protein sequence and functional information National Center for Biotechnology Information, United States National Library of Medicine National Institute of Genetics Swiss Institute of Bioinformatics Australia Bioinformatics Resource European Molecular Biology Organization European Nucleotide Archive Official website
A patch is a set of changes to a computer program or its supporting data designed to update, fix, or improve it. This includes fixing security vulnerabilities and other bugs, with such patches being called bugfixes or bug fixes, improving the usability or performance. Although meant to fix problems, poorly designed patches can sometimes introduce new problems. In some special cases updates may knowingly break the functionality or disable a device, for instance, by removing components for which the update provider is no longer licensed. Patch management is a part of lifecycle management, is the process of using a strategy and plan of what patches should be applied to which systems at a specified time. Patches for proprietary software are distributed as executable files instead of source code; this type of patch modifies the program executable—the program the user runs—either by modifying the binary file to include the fixes or by replacing it. On early 8-bit microcomputers, for example the Radio Shack TRS-80, the operating system included a PATCH utility which accepted patch data from a text file and applied the fixes to the target program's executable binary file.
Small in-memory patches could be manually applied with the system debug utility, such as CP/M's DDT or MS-DOS's DEBUG debuggers. Programmers working in interpreted BASIC used the POKE command to temporarily alter the functionality of a system service routine. Patches can circulate in the form of source code modifications. In this case, the patches consist of textual differences between two source code files, called "diffs"; these types of patches come out of open-source software projects. In these cases, developers expect users to compile the changed files themselves; because the word "patch" carries the connotation of a small fix, large fixes may use different nomenclature. Bulky patches or patches that change a program may circulate as "service packs" or as "software updates". Microsoft Windows NT and its successors use the "service pack" terminology. IBM used the terms "FixPaks" and "Corrective Service Diskette" to refer to these updates. Software suppliers distributed patches on paper tape or on punched cards, expecting the recipient to cut out the indicated part of the original tape, patch in the replacement segment.
Patch distributions used magnetic tape. After the invention of removable disk drives, patches came from the software developer via a disk or CD-ROM via mail. With the available Internet access, downloading patches from the developer's web site or through automated software updates became available to the end-users. Starting with Apple's Mac OS 9 and Microsoft's Windows ME, PC operating systems gained the ability to get automatic software updates via the Internet. Computer programs can coordinate patches to update a target program. Automation simplifies the end-user's task – they need only to execute an update program, whereupon that program makes sure that updating the target takes place and correctly. Service packs for Microsoft Windows NT and its successors and for many commercial software products adopt such automated strategies; some programs can update themselves via the Internet with little or no intervention on the part of users. The maintenance of server software and of operating systems takes place in this manner.
In situations where system administrators control a number of computers, this sort of automation helps to maintain consistency. The application of security patches occurs in this manner; the size of patches may vary from a few bytes to hundreds of megabytes. In particular, patches can become quite large when the changes add or replace non-program data, such as graphics and sounds files; such situations occur in the patching of computer games. Compared with the initial installation of software, patches do not take long to apply. In the case of operating systems and computer server software, patches have the important role of fixing security holes; some critical patches involve issues with drivers. Patches may require prior application of other patches, or may require prior or concurrent updates of several independent software components. To facilitate updates, operating systems provide automatic or semi-automatic updating facilities. Automatic updates have not succeeded in gaining widespread popularity in corporate computing environments because of the aforementioned glitches, but because administrators fear that software companies may gain unlimited control over their computers.
Package management systems can offer various degrees of patch automation. Usage of automatic updates has become far more widespread in the consumer market, due to the fact that Microsoft Windows added support for them, Service Pack 2 of Windows XP enabled them by default. Cautious users system administrators, tend to put off applying patches until they can verify the stability of the fixes. Microsoft SUS supports this. In the cases of large patches or of significant changes, distributors limit availability of patches to qualified developers as a beta test. Applying patches to firmware poses special challenges, as it involves the provisioning of new firmware images, rather than applying only the differences from the previous version; the patch consists of a firmware image in form of binary d
Open-source software is a type of computer software in which source code is released under a license in which the copyright holder grants users the rights to study and distribute the software to anyone and for any purpose. Open-source software may be developed in a collaborative public manner. Open-source software is a prominent example of open collaboration. Open-source software development generates an more diverse scope of design perspective than any company is capable of developing and sustaining long term. A 2008 report by the Standish Group stated that adoption of open-source software models have resulted in savings of about $60 billion per year for consumers. In the early days of computing and developers shared software in order to learn from each other and evolve the field of computing; the open-source notion moved to the way side of commercialization of software in the years 1970-1980. However, academics still developed software collaboratively. For example Donald Knuth in 1979 with the TeX typesetting system or Richard Stallman in 1983 with the GNU operating system.
In 1997, Eric Raymond published The Cathedral and the Bazaar, a reflective analysis of the hacker community and free-software principles. The paper received significant attention in early 1998, was one factor in motivating Netscape Communications Corporation to release their popular Netscape Communicator Internet suite as free software; this source code subsequently became the basis behind SeaMonkey, Mozilla Firefox and KompoZer. Netscape's act prompted Raymond and others to look into how to bring the Free Software Foundation's free software ideas and perceived benefits to the commercial software industry, they concluded that FSF's social activism was not appealing to companies like Netscape, looked for a way to rebrand the free software movement to emphasize the business potential of sharing and collaborating on software source code. The new term they chose was "open source", soon adopted by Bruce Perens, publisher Tim O'Reilly, Linus Torvalds, others; the Open Source Initiative was founded in February 1998 to encourage use of the new term and evangelize open-source principles.
While the Open Source Initiative sought to encourage the use of the new term and evangelize the principles it adhered to, commercial software vendors found themselves threatened by the concept of distributed software and universal access to an application's source code. A Microsoft executive publicly stated in 2001 that "open source is an intellectual property destroyer. I can't imagine something that could be worse than this for the software business and the intellectual-property business." However, while Free and open-source software has played a role outside of the mainstream of private software development, companies as large as Microsoft have begun to develop official open-source presences on the Internet. IBM, Oracle and State Farm are just a few of the companies with a serious public stake in today's competitive open-source market. There has been a significant shift in the corporate philosophy concerning the development of FOSS; the free-software movement was launched in 1983. In 1998, a group of individuals advocated that the term free software should be replaced by open-source software as an expression, less ambiguous and more comfortable for the corporate world.
Software licenses grant rights to users which would otherwise be reserved by copyright law to the copyright holder. Several open-source software licenses have qualified within the boundaries of the Open Source Definition; the most prominent and popular example is the GNU General Public License, which "allows free distribution under the condition that further developments and applications are put under the same licence", thus free. The open source label came out of a strategy session held on April 7, 1998 in Palo Alto in reaction to Netscape's January 1998 announcement of a source code release for Navigator. A group of individuals at the session included Tim O'Reilly, Linus Torvalds, Tom Paquin, Jamie Zawinski, Larry Wall, Brian Behlendorf, Sameer Parekh, Eric Allman, Greg Olson, Paul Vixie, John Ousterhout, Guido van Rossum, Philip Zimmermann, John Gilmore and Eric S. Raymond, they used the opportunity before the release of Navigator's source code to clarify a potential confusion caused by the ambiguity of the word "free" in English.
Many people claimed that the birth of the Internet, since 1969, started the open-source movement, while others do not distinguish between open-source and free software movements. The Free Software Foun
Christoph Steinbeck is a chemist born in Neuwied in 1966 and has a professorship for analytical chemistry and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia, Germany. Steinbeck received his PhD from the University of Bonn in 1995 for work on LUCY, a software program for structural elucidation from nuclear magnetic resonance correlation experiments. In 2003 he received his habilitation. Steinbeck's research interests have involved the elucidation of chemical structures of metabolites, he was one of the first chemists to develop open source tools for cheminformatics. He initiated JChemPaint, was founder of the Chemistry Development Kit, is responsible for leading the team working on Chemical Entities of Biological Interest, he headed the Cheminformatics and Metabolomics group at the European Molecular Biology Laboratory-European Bioinformatics Institute in Cambridge, United Kingdom from 2008 to 2016. He became a professor for analytical chemistry and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia, Germany in March 2017.
Together with a few other chemists he was a founder member of the Blue Obelisk movement in 2005. Steinbeck is editor-in-chief of the Journal of Cheminformatics, director of the Metabolomics Society, past chair of the Computers-Information-Chemistry division of the German Chemical Society, past trustee of the Chemical Structure Association Trust, a lifetime member of the World Association of Theoretically Oriented Chemists. Www.steinbeck-molecular.de www.ebi.ac.uk/steinbeck