scholarly journals Open Source Research — the Power of Us

2006 ◽  
Vol 59 (5) ◽  
pp. 291 ◽  
Author(s):  
Thomas B. Kepler ◽  
Marc A. Marti-Renom ◽  
Stephen M. Maurer ◽  
Arti K. Rai ◽  
Ginger Taylor ◽  
...  
Keyword(s):  
Organic Chemistry ◽  
Computer Science ◽  
Open Source ◽  
Peer Review ◽  
Biomedical Research ◽  
Specific Problem ◽  
Scientific Research ◽  
Great Promise ◽  
Competitive Funding ◽  
Science Community

Academic and industrial scientific research operate on powerful and complementary models, consisting of some mix of competitive funding, peer review, and limited inter-laboratory collaboration. Enormous successes have arisen from both models. Yet there are clear failures to deliver results in certain areas, such as the provision of drugs for some of the most prevalent of human diseases. Is there a mechanism of research that is not wholly dependent on funding for its operation nor on traditional peer-reviewed articles for its propagation? Open source methods have delivered tangible benefits in the computer science community. We describe here efforts to extend these principles to science generally, and in particular biomedical research. Open source research holds great promise for solving complex problems in areas where profit-driven research is seen to have failed. We illustrate this with a specific problem in organic chemistry that we think will be solved substantially faster with an open source approach.

scholarly journals CHIC: a short read aligner for pan-genomic references

2017 ◽  
Author(s):  
Daniel Valenzuela ◽  
Veli Mäkinen
Keyword(s):  
Computer Science ◽  
Open Source ◽  
Bioinformatic Analysis ◽  
Hybrid Technique ◽  
Short Read ◽  
Pan Genome ◽  
Link Type ◽  
Short Read Aligner ◽  
Science Community

AbstractRecently the topic of computational pan-genomics has gained increasing attention, and particularly the problem of moving from a single-reference paradigm to a pan-genomic one. Perhaps the simplest way to represent a pan-genome is to represent it as a set of sequences. While indexing highly repetitive collections has been intensively studied in the computer science community, the research has focused on efficient indexing and exact pattern patching, making most solutions not yet suitable to be used in bioinformatic analysis pipelines.Results:We present CHIC, a short-read aligner that indexes very large and repetitive references using a hybrid technique that combines Lempel-Ziv compression with Burrows-Wheeler read aligners.Availability:Our tool is open source and available online at https://gitlab.com/dvalenzu/CHIC

scholarly journals Leveraging Final Degree Projects for Open Source Software Contributions

Electronics ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1181
Author(s):  
Juanan Pereira
Keyword(s):  
Graduate Students ◽  
Software Engineering ◽  
Computer Science ◽  
Open Source ◽  
Communication Skills ◽  
Open Source Software ◽  
Real World ◽  
Practical Experience ◽  
Multiple Challenges ◽  
Final Degree

(1) Background: final year students of computer science engineering degrees must carry out a final degree project (FDP) in order to graduate. Students’ contributions to improve open source software (OSS) through FDPs can offer multiple benefits and challenges, both for the students, the instructors and for the project itself. This work reports on a practical experience developed by four students contributing to mature OSS projects during their FDPs, detailing how they addressed the multiple challenges involved, both from the students and teachers perspective. (2) Methods: we followed the work of four students contributing to two established OSS projects for two academic years and analyzed their work on GitHub and their responses to a survey. (3) Results: we obtained a set of specific recommendations for future practitioners and detailed a list of benefits achieved by steering FDP towards OSS contributions, for students, teachers and the OSS projects. (4) Conclusion: we find out that FDPs oriented towards enhancing OSS projects can introduce students into real-world, practical examples of software engineering principles, give them a boost in their confidence about their technical and communication skills and help them build a portfolio of contributions to daily used worldwide open source applications.

Collaboration, peer review and open source software

2006 ◽  
Vol 18 (4) ◽  
pp. 477-497 ◽  
Author(s):  
Justin P. Johnson
Keyword(s):  
Open Source ◽  
Peer Review ◽  
Open Source Software

Creating a national K--12 computer science community

2005 ◽  
Vol 48 (1) ◽  
pp. 29-31 ◽  
Author(s):  
Chris Stephenson
Keyword(s):  
Computer Science ◽  
Science Community ◽  
K 12

Modern trends in the development of organic chemistry

2021 ◽  
pp. 71-78
Author(s):  
Irina Anatolievna Selivanova ◽  
Roman Petrovich Terekhov ◽  
Amir Khalilovich Taldaev
Keyword(s):  
Organic Chemistry ◽  
Pharmaceutical Industry ◽  
Scientific Research ◽  
Modern World ◽  
International Conference ◽  
Qualified Personnel ◽  
Scientific Potential ◽  
Young Researchers

The role of organic chemistry and other chemical disciplines in the system of training qualified personnel for the pharmaceutical industry is indisputable. In what direction is chemistry developing in the modern world? What innovative directions does chemistry offer to drug developers? Can a robot synthesize a new compound? How to achieve practically significant results of scientific research? How may the obtained results be published in highly rated journals? These and many other topics were widely discussed at the XII International Conference of Students and Young Scientists in Chemistry «Mendeleev-2021» held in the fall of 2021. This article is published to attract young researchers’ attention to topical issues at the interface of chemistry and pharmacy and assist them in realizing their creative scientific potential.

scholarly journals Sleep and BMI: Do (Fitbit) bands aid?

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 511 ◽  
Author(s):  
Laura McDonald ◽  
Faisal Mehmud ◽  
Sreeram V. Ramagopalan
Keyword(s):  
Body Mass Index ◽  
Body Mass ◽  
Biomedical Research ◽  
Chinese Population ◽  
Scientific Research ◽  
Negatively Associated ◽  
Significant Potential ◽  
Consumer Devices

Recent studies have used mainstream consumer devices (Fitbit) to assess sleep objectively and test the well documented association between sleep and body mass index (BMI). In order to further investigate the applicability of Fitbit data for biomedical research across the globe, we analysed openly available Fitbit data from a largely Chinese population. We found that after adjusting for age, gender, race, and average number of steps taken per day, average hours of sleep per day was negatively associated with BMI (p=0.02), further demonstrating the significant potential for wearables in international scientific research.

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