Publishing data and code openly

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Written and presented by Tom Ingraham (F1000), at the Reproducible and Citable Data and Model Workshop, in Warnemünde, Germany. September 14th -16th 2015.

Ciencias

Thomas Ingraham
Publishing Editor, F1000Research
thomas.ingraham@f1000.com

Enabling early access to results
Pre-print server OA Journal
Early access to results & data Editorial input
Precedence for authors Peer review & indexing
Multiple versions Publication ethics
No Editor in Chief Perfected paper OA

Open peer review
Decision based on
scientific soundness

publishing raw data and source code
Uses
•Exploratory analyses, LOD, reproducibility checks (data,
reanalyses + software)
Linking with Research Articles
•Better metadata/documentation
•Quality control
Software Tool Articles & Data Articles
•Big/small datasets – no analyses
•Software packages/web tools
•Even better metadata/documentation
•Versioning – updates & point releases
•High visibility
•More credit (quantity and quality)

Requirements for data and code
Interoperable formats
Metadata
All?

Workflow & repositories
Submission
Pre-Pub
Check
Publish
Peer
review
Repository
Crosslink
Further requests
F1000Research
curates approved
repo list

Credit for data and software
Data availability:
Repository: Data entry title, PID [Ref]
[Ref] Author Names. Data entry title [v].
Repository. Year. PID
Cite the data or the Data Article?
Clear accessibility info and actively encourage data/software citation
Software availability:
Software access (opt): URL
Latest source code (opt): VCS URL
Archived entry: Repository: Software
title, PID [Ref]
Licence: OSI
[Ref] Author Names. Software title [v].
Repository. Year. PID

INTERGRATION, VISUALIZATION & ANALYSIS OF DATA

Living figures: Data + Code
Colomb & Brembs: http://f1000research.com/articles/3-176/v1

Challenges
Sensitive data
•Protected repositories
•HIPPA-compliant (safe harbour)
•DataSHIELD
Other challenges
•Rawness & granularity

Jisc Bodleian 1-click data submission Project
Reducing the friction data sharing

SUMMARY: F1000RESEARCH’S APPROACH TO OPEN SCIENCE
• Near-immediate publication
Open, invited peer review conducted after
publication
• Transparent peer-review
Signed referee reports and author responses
published alongside each article
• No editorial bias
Publication of all findings, including null results,
software tools and data notes.
• Data included
All research articles accompanied by the data on
which they are based

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Pests of cotton_Sucking_Pests_Dr.UPR.pdf

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SCIENCE-4-QUARTER4-WEEK-4-PPT-1 (1).pptx

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Conjugation, transduction and transformation

Areesha Ahmad

Mustard, as a crop, is susceptible to a variety of pests that can affect its growth and yield. Here’s a rundown of some common pests that target mustard plants: Aphids: These small, sap-sucking insects can cause significant damage by feeding on the leaves and stems. Aphids also excrete a sticky substance known as honeydew, which can lead to the growth of sooty mold on the plants. Flea Beetles: These tiny beetles jump like fleas when disturbed and chew small holes in the leaves. They are particularly damaging in the early growth stages of the plant. Cabbage Loopers: The larvae of a type of moth, these caterpillars are known for their distinctive looping movement. They chew large holes in the leaves and can defoliate plants if present in large numbers. Diamondback Moth Larvae: Another caterpillar pest, these larvae chew small holes in the leaves and can cause extensive damage, especially when infestations are heavy. Whiteflies: These are tiny, winged insects that feed on plant sap and can quickly become a problem in greenhouse or close planting conditions. Like aphids, they also secrete honeydew. Cutworms: These are the larvae of certain types of moths and are known for cutting young plants at the stem base at ground level. They are most destructive during the night. Root Maggots: The larvae of root maggot flies, these pests attack the roots of mustard plants, causing wilting and potentially killing young plants. Harlequin Bugs: These are colorful stink bugs that suck the sap from mustard plant stems and leaves, causing the leaves to become stippled, wilt, and eventually die if the infestation is severe. Mustard Sawfly: The larvae of the mustard sawfly can cause considerable defoliation, as they feed voraciously on the leaves. Clubroot: Caused by a fungus-like organism, clubroot affects the roots, causing them to swell and distort. While technically a disease, it is often associated with pest management because controlling it involves similar preventative strategies. Control Measures: Managing pests in mustard involves a combination of cultural, biological, and chemical methods. Crop rotation, resistant varieties, timely sowing, maintaining plant health, and using natural predators like ladybugs and parasitic wasps can help keep pest populations under control. Chemical pesticides should be used as a last resort due to their potential impact on the environment and non-target species.

Pests of mustard_Identification_Management_Dr.UPR.pdf

PirithiRaju

CELL -Structural and Functional unit of life.pdf

Nistarini College, Purulia (W.B) India

The computation of anti-derivatives is just an in-tellectual challenge, we know how to take deriv-atives, but … can we invert the process? We call this Computing the indefinite integral . In the last presentation we have seen a few indefinite integrals (we called them bricks), but they did not include the anti-derivative of many functions! We are going to try and do better !

COMPUTING ANTI-DERIVATIVES(Integration by SUBSTITUTION)

AkefAfaneh2

Theoretical predictions and observational data indicate a class of sub-Neptune exoplanets may have water-rich interiors covered by hydrogen-dominated atmospheres. Provided suitable climate conditions, such planets could host surface liquid oceans. Motivated by recent JWST observations of K2-18 b, we self-consistently model the photochemistry and potential detectability of biogenic sulfur gases in the atmospheres of temperate sub-Neptune waterworlds for the first time. On Earth today, organic sulfur compounds produced by marine biota are rapidly destroyed by photochemical processes before they can accumulate to significant levels. Domagal-Goldman et al. suggest that detectable biogenic sulfur signatures could emerge in Archean-like atmospheres with higher biological production or low UV flux. In this study, we explore biogenic sulfur across a wide range of biological fluxes and stellar UV environments. Critically, the main photochemical sinks are absent on the nightside of tidally locked planets. To address this, we further perform experiments with a 3D general circulation model and a 2D photochemical model (VULCAN 2D) to simulate the global distribution of biogenic gases to investigate their terminator concentrations as seen via transmission spectroscopy. Our models indicate that biogenic sulfur gases can rise to potentially detectable levels on hydrogen-rich water worlds, but only for enhanced global biosulfur flux (20 times modern Earth’s flux). We find that it is challenging to identify DMS at 3.4 μm where it strongly overlaps with CH4, whereas it is more plausible to detect DMS and companion byproducts, ethylene (C2H4) and ethane (C2H6), in the mid-infrared between 9 and 13 μm. Unified Astronomy Thesaurus concepts: Exoplanet atmospheres (487); Exoplanet

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Sérgio Sacani

Publishing data and code openly

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