OpenCon2014 - Sumatra as an Open Science tool

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The document discusses Sumatra, an open source tool for reproducible research in computational projects. Sumatra captures information about the code version, input data, output data, and parameters of a computational experiment to allow full replication of results. By tracking data provenance throughout a research project, Sumatra aims to address common challenges to reproducibility like unclear documentation of methods and parameters over time.

-as an Open Science tool
Presented by
Felix Hoffmann
@Felix11H
felix11h.github.io/
Slides
Slideshare:
tiny.cc/opencon-smt
Source:
tiny.cc/github-slides
Resources on Sumatra
Website:
neuralensemble.org/sumatra/
Getting started:
packages.python.org/Sumatra/
Repository:
bitbucket.org/apdavison/sumatra/
Mailinglist:
tiny.cc/smt-user
Maintainer: Andrew Davison
This work is licensed under a Creative Commons Attribution 4.0 International License.

Spectrum of Reproducibility
... in Computational Research
—–

Spectrum of Reproducibility
... in Computational Research
reproduction from
descriptions in
research article
—–

Spectrum of Reproducibility
... in Computational Research
reproduction from
descriptions in
research article
—–Tough!
—–

Spectrum of Reproducibility
... in Computational Research
reproduction from
descriptions in
research article
—–Tough!
same code,
—–
—–

Spectrum of Reproducibility
... in Computational Research
reproduction from
descriptions in
research article
—–Tough!
same code,
same machine, —–
—–

Spectrum of Reproducibility
... in Computational Research
reproduction from
descriptions in
research article
—–Tough!
same code,
same machine, —–
same researcher
—–

The problems...
Which version of my
code did I use?
“Piled Higher and Deeper” by Jorge Cham
www.phdcomics.com

The problems...
Which version of my
code did I use?
What parameters?
“Piled Higher and Deeper” by Jorge Cham
www.phdcomics.com

The problems...
Which version of my
code did I use?
What parameters?
“Why did I do that?”
“Piled Higher and Deeper” by Jorge Cham
www.phdcomics.com

The problems...
Which version of my
code did I use?
What parameters?
“Why did I do that?”
“It worked yesterday.”
“Piled Higher and Deeper” by Jorge Cham
www.phdcomics.com

The problems... ... the solution –
Which version of my
code did I use?
What parameters?
“Why did I do that?”
“It worked yesterday.”

The problems... ... the solution –
Which version of my
code did I use?
What parameters?
“Why did I do that?”
“It worked yesterday.”
laboratory notebook
©Wellcome Library, London CC BY 4.0

-- -Simulation Management Tool
“An automated lab notebook for
computational projects”

-- -Simulation Management Tool
“An automated lab notebook for
computational projects”
) assumes that code is under
version control
©Jason Long CC BY 3.0

-- -Simulation Management Tool
“An automated lab notebook for
computational projects”
) assumes that code is under
version control
) capture information about
computation
smt run

- -- a tool for Reproducible Research
By capturing

- -- a tool for Reproducible Research
By capturing
- version of the code

- -- a tool for Reproducible Research
By capturing
- version of the code
- input data

- -- a tool for Reproducible Research
By capturing
- version of the code
- input data
- output data

- -- a tool for Reproducible Research
By capturing
- version of the code
- input data
- output data
- parameters ————

- -- a tool for Reproducible Research
By capturing
- version of the code
- input data
- output data
- parameters ————
9>>>>>>>>>=
>>>>>>>>>;
Full replicability of
results

- -- as an Open Science tool
computational r.esearch project

- -- as an Open Science tool
computational r.esearch project
scientific code

- -- as an Open Science tool
computational r.esearch project
scientific code
.
input data

- -- as an Open Science tool
computational r.esearch project
scientific code
.
input data
output data

- -- as an Open Science tool
computational r.esearch project
scientific code
.
input data
output data
Data
provenance!

Thank you!
Presented by
Felix Hoffmann
@Felix11H
felix11h.github.io/
Slides
Slideshare:
tiny.cc/opencon-smt
Source:
tiny.cc/github-slides
Resources on Sumatra
Website:
neuralensemble.org/sumatra/
Getting started:
packages.python.org/Sumatra/
Repository:
bitbucket.org/apdavison/sumatra/
Mailinglist:
tiny.cc/smt-user
Maintainer: Andrew Davison
This work is licensed under a Creative Commons Attribution 4.0 International License.

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原版纸张【微信：741003700 】【(carleton毕业证书)卡尔顿大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...

Travis Hills MN

Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.

ESR spectroscopy in liquid food and beverages.pptx

PRIYANKA PATEL

With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.

Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...

AbdullaAlAsif1

The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.

Cytokines and their role in immune regulation.pptx

Hitesh Sikarwar

如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样

yqqaatn0

原版纸张【微信：741003700 】【(uvic毕业证书)维多利亚大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma 1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700 留信网认证的作用: 1:该专业认证可证明留学生真实身份 2:同时对留学生所学专业登记给予评定 3:国家专业人才认证中心颁发入库证书 4:这个认证书并且可以归档倒地方 5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息 6:个人职称评审加20分 7:个人信誉贷款加10分 8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才

Thornton ESPP slides UK WW Network 4_6_24.pdf

European Sustainable Phosphorus Platform

Basics of crystallography, crystal systems, classes and different forms

MaheshaNanjegowda

Authoring a personal GPT for your research and practice: How we created the Q...

Leonel Morgado

Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.

SAR of Medicinal Chemistry 1st by dk.pdf

KrushnaDarade1

Micronuclei test.M.sc.zoology.fisheries.

Aditi Bajpai

Compexometric titration/Chelatorphy titration/chelating titration

Vandana Devesh Sharma

Classification Metal ion ion indicators Masking and demasking reagents Estimation of Magnisium sulphate Calcium gluconate Complexometric Titration/ chelatometry titration/chelating titration, introduction, Types- 1.Direct Titration 2.Back Titration 3.Replacement Titration 4.Indirect Titration Masking agent, Demasking agents formation of complex comparition between masking and demasking agents, Indicators/Metal ion indicators/ Metallochromic indicators/pM indicators, Visual Technique,PM indicators (metallochromic), Indicators of pH, Redox Indicators Instrumental Techniques-Photometry Potentiometry Miscellaneous methods. Complex titration with EDTA.

Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf

TinyAnderson

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原版制作(carleton毕业证书)卡尔顿大学毕业证硕士文凭原版一模一样

Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...

ESR spectroscopy in liquid food and beverages.pptx

Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...

Cytokines and their role in immune regulation.pptx

如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样

Thornton ESPP slides UK WW Network 4_6_24.pdf

Basics of crystallography, crystal systems, classes and different forms

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SAR of Medicinal Chemistry 1st by dk.pdf

Micronuclei test.M.sc.zoology.fisheries.

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Topic: SICKLE CELL DISEASE IN CHILDREN-3.pdf

OpenCon2014 - Sumatra as an Open Science tool

1. -as an Open Science tool Presented by Felix Hoffmann @Felix11H felix11h.github.io/ Slides Slideshare: tiny.cc/opencon-smt Source: tiny.cc/github-slides Resources on Sumatra Website: neuralensemble.org/sumatra/ Getting started: packages.python.org/Sumatra/ Repository: bitbucket.org/apdavison/sumatra/ Mailinglist: tiny.cc/smt-user Maintainer: Andrew Davison This work is licensed under a Creative Commons Attribution 4.0 International License.

2. Spectrum of Reproducibility ... in Computational Research —–

3. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–

4. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! —–

5. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, —– —–

6. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, same machine, —– —–

7. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, same machine, —– same researcher —–

8. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, same machine, —– same researcher —– Easy!

9. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, same machine, —– same researcher —– Easy! if only!

10. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, same machine, —– same researcher —– Easy! if only!

11. Spectrum of Reproducibility ... in Computational Research reproduction from descriptions in research article —–Tough! same code, same machine, —– same researcher —– Easy! if only!

12. The problems... Which version of my code did I use? “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

13. The problems... Which version of my code did I use? What parameters? “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

14. The problems... Which version of my code did I use? What parameters? “Why did I do that?” “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

15. The problems... Which version of my code did I use? What parameters? “Why did I do that?” “It worked yesterday.” “Piled Higher and Deeper” by Jorge Cham www.phdcomics.com

16. The problems... ... the solution – Which version of my code did I use? What parameters? “Why did I do that?” “It worked yesterday.”

17. The problems... ... the solution – Which version of my code did I use? What parameters? “Why did I do that?” “It worked yesterday.” laboratory notebook ©Wellcome Library, London CC BY 4.0

18. The problems... ... the solution – Which version of my code did I use? What parameters? “Why did I do that?” “It worked yesterday.” laboratory notebook ©Wellcome Library, London CC BY 4.0 ... in traditional, experiment-based research.

19. -- -Simulation Management Tool

20. -- -Simulation Management Tool “An automated lab notebook for computational projects”

21. -- -Simulation Management Tool “An automated lab notebook for computational projects”

22. -- -Simulation Management Tool “An automated lab notebook for computational projects” ) assumes that code is under version control ©Jason Long CC BY 3.0

23. -- -Simulation Management Tool “An automated lab notebook for computational projects” ) assumes that code is under version control ) capture information about computation smt run

24. -- -Simulation Management Tool “An automated lab notebook for computational projects” ) assumes that code is under version control ) capture information about computation ) make the information accessible through a command line and web interface

25. - -- a tool for Reproducible Research By capturing

26. - -- a tool for Reproducible Research By capturing - version of the code

27. - -- a tool for Reproducible Research By capturing - version of the code - input data

28. - -- a tool for Reproducible Research By capturing - version of the code - input data - output data

29. - -- a tool for Reproducible Research By capturing - version of the code - input data - output data - parameters ————

30. - -- a tool for Reproducible Research By capturing - version of the code - input data - output data - parameters ———— 9>>>>>>>>>= >>>>>>>>>; Full replicability of results

31. - -- as an Open Science tool computational r.esearch project

32. - -- as an Open Science tool computational r.esearch project scientific code

33. - -- as an Open Science tool computational r.esearch project scientific code . input data

34. - -- as an Open Science tool computational r.esearch project scientific code . input data output data

35. - -- as an Open Science tool computational r.esearch project scientific code . input data output data

36. - -- as an Open Science tool computational r.esearch project scientific code . input data output data

37. - -- as an Open Science tool computational r.esearch project scientific code . input data output data

38. - -- as an Open Science tool computational r.esearch project scientific code . input data output data

39. - -- as an Open Science tool computational r.esearch project scientific code . input data output data Data provenance!

40. Thank you! Presented by Felix Hoffmann @Felix11H felix11h.github.io/ Slides Slideshare: tiny.cc/opencon-smt Source: tiny.cc/github-slides Resources on Sumatra Website: neuralensemble.org/sumatra/ Getting started: packages.python.org/Sumatra/ Repository: bitbucket.org/apdavison/sumatra/ Mailinglist: tiny.cc/smt-user Maintainer: Andrew Davison This work is licensed under a Creative Commons Attribution 4.0 International License.

OpenCon2014 - Sumatra as an Open Science tool

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