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Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software

Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope
2019 GigaScience  
Background Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of
more » ... urces; lack of reproducibility, usability, adaptability, and interoperability; and erroneous or inaccurate results. Findings We have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages. The resulting software is functional, carrying out a prototypical bioinformatics task, and thus serves as both a working example and a template for building new tools. Key features include command-line argument parsing, error handling, progress logging, defined exit status values, a test suite, a version number, standardized building and packaging, user documentation, code documentation, a standard open source software license, software revision control, and containerization. Conclusions Bionitio serves as a learning aid for beginner-to-intermediate bioinformatics programmers and provides an excellent starting point for new projects. This helps developers adopt good programming practices from the beginning of a project and encourages high-quality tools to be developed more rapidly. This also benefits users because tools are more easily installed and consistent in their usage. Bionitio is released as open source software under the MIT License and is available at https://github.com/bionitio-team/bionitio.
doi:10.1093/gigascience/giz109 pmid:31544213 pmcid:PMC6755254 fatcat:6o6iyirqvfemtkd2oaegnkvddy

Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud

Enis Afgan, Clare Sloggett, Nuwan Goonasekera, Igor Makunin, Derek Benson, Mark Crowe, Simon Gladman, Yousef Kowsar, Michael Pheasant, Ron Horst, Andrew Lonie, Christophe Antoniewski
2015 PLoS ONE  
Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible,
more » ... oducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.
doi:10.1371/journal.pone.0140829 pmid:26501966 pmcid:PMC4621043 fatcat:6s4gje7sr5eotjs6yfju7ae5hu

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján (+16 others)
2014 BMC Bioinformatics  
Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by
more » ... formal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.
doi:10.1186/1471-2105-15-s14-s7 pmid:25472764 pmcid:PMC4255748 fatcat:p7jbtuipnbdafo3zauaqrhu5sq

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

Matthew K.H. Hong, Geoff Macintyre, David C. Wedge, Peter Van Loo, Keval Patel, Sebastian Lunke, Ludmil B. Alexandrov, Clare Sloggett, Marek Cmero, Francesco Marass, Dana Tsui, Stefano Mangiola (+17 others)
2015 Nature Communications  
Tumour heterogeneity in primary prostate cancer is a well-established phenomenon. However, how the subclonal diversity of tumours changes during metastasis and progression to lethality is poorly understood. Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic tumours. We find one case of metastatic spread to the surgical bed causing local
more » ... rence, and another case of crossmetastatic site seeding combining with dynamic remoulding of subclonal mixtures in response to therapy. By ultra-deep sequencing end-stage blood, we detect both metastatic and primary tumour clones, even years after removal of the prostate. Analysis of mutations associated with metastasis reveals an enrichment of TP53 mutations, and additional sequencing of metastases from 19 patients demonstrates that acquisition of TP53 mutations is linked with the expansion of subclones with metastatic potential which we can detect in the blood.
doi:10.1038/ncomms7605 pmid:25827447 pmcid:PMC4396364 fatcat:dzg274r5nzc67fvb7phhxoyvpu

Path integral Monte Carlo approach to the U(1) lattice gauge theory in 2+1 dimensions

Mushtaq Loan, Michael Brunner, Clare Sloggett, Chris Hamer
2003 Physical Review D, Particles and fields  
Path Integral Monte Carlo simulations have been performed for U(1) lattice gauge theory in (2+1) dimensions on anisotropic lattices. We extractthe static quark potential, the string tension and the low-lying "glueball" spectrum.The Euclidean string tension and mass gap decrease exponentially at weakcoupling in excellent agreement with the predictions of Polyakov and Göpfert and Mack, but their magnitudes are five times bigger than predicted. Extrapolations are made to the extreme anisotropic or
more » ... Hamiltonian limit, and comparisons are made with previous estimates obtained in the Hamiltonian formulation.
doi:10.1103/physrevd.68.034504 fatcat:fzsc5kw56ffa3mgvfnzopzhfb4

Page 325 of European Journal of Cancer Care Vol. 12, Issue 4 [page]

2003 European Journal of Cancer Care  
., Charmain Ponnuthurai of Macmillan for her invaluable contribution to the formation, planning and conduct of the study, Deanna Buick of Macmillan for her comments on an earlier draft, Clare Moynihan  ...  Coleman M.P., Babb P., Damiecki P., Grosclaude P., Honjo S., Jones J., Knerer G., Pitard A., Quinn M., Sloggett A. & De Stavola A. (1999) Cancer survival trends in England and Wales 1971-1995: deprivation  ... 

Page 775 of The Gentleman's Magazine Vol. 219, Issue [page]

1865 The Gentleman's Magazine  
Clare, a dau. j In Chester-sq., the wife of the Rev. John H. Snowden, a son, At the Leys, Farnborough, Kent, the wife of Henry J. Latter, esq., a dau.  ...  Charles Sloggett, a son. Nov. 1, In Lowndes-st., the Viscountess Malden, a son. . At Holmwood, Hinton, near Bath, the wife of Capt. Henry Raby, V.C., R.N., a son.  ... 

Page 510 of The Lancet Vol. 1, Issue 3782 [page]

1896 The Lancet  
Sloggett. The under-mentioned Surgeon-Lieutenants to be Surgeon-Captains (dated Jan. 30th, 1896) :—Frederick M. Mangan, Charles E. Pollock, William J. Taylor, M.B., Bell W. Longhurst. John H.  ...  Clare Carruthers. Surgeon-Major H. Thomson, M.B., is appointed to be Civil Surgeon, Coconada, in succession to Surgeon- Major J. C. Marsden. NAVAL MEDICAL SERVICE.  ... 

Medical News

1904 The Lancet  
Lucas, B.A., Clare; S. M. Mackenzie, B.A., Trinity; C. W. P. Moffatt, B.A., Clare; W. M. Mollison, B.A., King's ; A. R. Moore, B.A., Caius; R. F. Moore, B.A., Christ's; W. V.  ...  Worthington, B.A., Clare. conferred on June 21st:- Bachelor of Medicine.-J. E. Pellow, St. John's; E. A. A. Beck, Clare; W. H. Hills, Pembroke ; J. S. Cooper, Jesus; G. S. Colt and J. B.  ... 
doi:10.1016/s0140-6736(01)47377-6 fatcat:ke2bg2eezrbglbt3twn4dxwbq4

The outsider anthropologist? Leonhard Adam in Germany and Melbourne

Michael Davis
2020 Australian Journal of Biography and History  
, 176. 43 Sloggett, '"Has Aboriginal Art a Future?"'  ...  Sloggett explains: There were good reasons for Adam to publish this essay in a new and experimental magazine.  ... 
doi:10.22459/ajbh.04.2020.06 fatcat:2p2cdg7rkncqlgzjyy22dlvfzq

Page 1015 of The Lancet Vol. 2, Issue 4337 [page]

1906 The Lancet  
The chairman's health was by Colonel Sloggett in warmly appreciative terms and was drunk enthusiastically. London Hospital.  ...  Clare Market had disappeared, and Drury-lane and all the slums associated therewith were being opened up and improved, so that the out-patient and casualty departments were steadily off in numbers.  ... 

Page 11 of British Medical Journal Vol. 2, Issue SUPPLEMENT [page]

1921 British Medical Journal  
Palmer, of the Hearts of Oak, who said he was _ not in favour of Government medical officers or their system, and de- clared that the panel system was bad enough without having it extended.  ...  Sloggett, K.C.B., K.C.M.G., K.C.V.O., ret. pay: Major-General Sir T. J. Gallwey, K.C.M.G., C.B., ret. pay; Surgeon- a gen (ranking as Major-General) Sir F. W. Trevor, K.C.S.I., C.B., ret. pay.  ... 

Page 589 of JAMA: The Journal of the American Medical Association Vol. 37, Issue 9 [page]

1901 JAMA: The Journal of the American Medical Association  
Sloggett, Cooper, Moore, Meyers, Sinclair and MeDonald. Mosquito-Infected Nurse Dies.  ...  Win- rate, Milwaukee, secretary of the State Board of Health, de- clared on August 20 that Wisconsin and all states of the middle \est would be swept by a scourge of malignant smallpox unless prompt and  ... 

THE WAR

1916 The BMJ (British Medical Journal) (Print)  
Clare, was educated at Quieen's College, Cork, and took the M.D., M.Cli., and the obstetrical diploma of the Royal University, Ire}and, in 1882, also the F.R.C.S.I. in 1890.  ...  Never before have two m-en had to undertalko a larger task or greater'responsibilities than those that have been slhouildered by Sir Arthur Sloggett and Sir Alfred Keogh respectively during the last eighteen  ... 
pmid:20768096 pmcid:PMC2347943 fatcat:me4kjwvvajhwhg3dap2ob6uary

THE SERVICES

1896 The Lancet  
Sloggett. The under-mentioned Surgeon-Lieutenants to be Surgeon-Captains (dated Jan. 30th, 1896) :-Frederick M. Mangan, Charles E. Pollock, William J. Taylor, M.B., Bell W. Longhurst. John H.  ...  Clare Carruthers. Surgeon-Major H. Thomson, M.B., is appointed to be Civil Surgeon, Coconada, in succession to Surgeon-Major J. C. Marsden. NAVAL MEDICAL SERVICE.  ... 
doi:10.1016/s0140-6736(01)93254-4 fatcat:l4gey6jwafbcvkmwoipxp2rtey
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