1. The document discusses tips and tools for data stewardship, including planning for data management, best practices for data collection and organization, documenting workflows, creating metadata, and sharing data.
2. It emphasizes writing a data management plan, keeping raw data separate and secure, using version control and backups, and revisiting plans periodically.
3. The document encourages learning skills for data management, using resources like libraries and repositories, and embracing changes that support more open and reproducible science.
NISO Webinar on data curation services at the CDLCarly Strasser
"Building communities and Services in Support of Data-Intensive Research". Webinar on 18 Sept 2013 for the NISO Webinar Series. This was part 2 of 2 for Data Curation
"Undergrad ecologists aren't learning data management" - ESA 2013Carly Strasser
Presentation for Ecological Society of America 2013 Meeting in Minneapolis, MN on 6 August 2013. Results published in Ecosphere doi: 10.1890/ES12-00139.1
NISO Webinar on data curation services at the CDLCarly Strasser
"Building communities and Services in Support of Data-Intensive Research". Webinar on 18 Sept 2013 for the NISO Webinar Series. This was part 2 of 2 for Data Curation
"Undergrad ecologists aren't learning data management" - ESA 2013Carly Strasser
Presentation for Ecological Society of America 2013 Meeting in Minneapolis, MN on 6 August 2013. Results published in Ecosphere doi: 10.1890/ES12-00139.1
Cal Poly - Data Management and the DMPToolCarly Strasser
October 17, 2013 @ Robert E. Kennedy Library, Data Studio, California Polytechnic State University.
Many funders now require researchers to submit a Data Management Plan alongside their project proposals. The DMPTool is a free, online wizard that helps you create a data management plan specific to your project, and provides you with links and resources for ensuring your plan is successful.
Cal Poly - Data Management for ResearchersCarly Strasser
October 17, 2013 @ 1 Robert E. Kennedy Library, Data Studio, California Polytechnic State University.
Researchers rarely learn about good data management practices. Instead we develop our own systems that are often unintelligible to others. In this talk, Strasser, PhD, will focus on the common mistakes that scientists make and how to avoid them. She will provide best practices for data management, which will facilitate data sharing and reuse, and introduce tools you can use.
Funders and publishers have something in common: for better or worse, we have the ability to influence the behavior of researchers. This talk will focus on what both groups can do to improve research now and in the future.
A Big Picture in Research Data ManagementCarole Goble
A personal view of the big picture in Research Data Management, given at GFBio - de.NBI Summer School 2018 Riding the Data Life Cycle! Braunschweig Integrated Centre of Systems Biology (BRICS), 03 - 07 September 2018
A talk I gave at the MMDS workshop June 2014 on the Myria system as well as some of Seung-Hee Bae's work on scalable graph clustering.
https://mmds-data.org/
Tools für das Management von ForschungsdatenHeinz Pampel
Workshop „Wege in die Köpfe“ des DFG-Projekts „EWIG - Entwicklung von Workflowkomponenten für die Langzeitarchivierung von Forschungsdaten in den Geowissenschaften“ | Berlin, 03.07.2014
Data Repositories: Recommendation, Certification and Models for Cost RecoveryAnita de Waard
Talk at NITRD Workshop "Measuring the Impact of Digital Repositories" February 28 – March 1, 2017 https://www.nitrd.gov/nitrdgroups/index.php?title=DigitalRepositories
DataShare - Pauline Ward to University of Edinburgh School of Chemistry - 3 f...University of Edinburgh
Talk targeted at researchers at the University of Edinburgh, explaining how they can use DataShare to publish their research results, and some of the benefits of doing so.
IDCC Workshop: Analysing DMPs to inform research data services: lessons from ...Amanda Whitmire
A workshop as part of the International Digital Curation Conference 2016 on DMP development and support. This presentation demonstrates how we can use data management plans as a source of information to better understand researcher data stewardship practices and how to support them. Be sure to see the slide notes to better understand the presentation (most slides are just photos/icons).
Keynote on software sustainability given at the 2nd Annual Netherlands eScience Symposium, November 2014.
Based on the article
Carole Goble ,
Better Software, Better Research
Issue No.05 - Sept.-Oct. (2014 vol.18)
pp: 4-8
IEEE Computer Society
http://www.computer.org/csdl/mags/ic/2014/05/mic2014050004.pdf
http://doi.ieeecomputersociety.org/10.1109/MIC.2014.88
http://www.software.ac.uk/resources/publications/better-software-better-research
Cal Poly - Data Management and the DMPToolCarly Strasser
October 17, 2013 @ Robert E. Kennedy Library, Data Studio, California Polytechnic State University.
Many funders now require researchers to submit a Data Management Plan alongside their project proposals. The DMPTool is a free, online wizard that helps you create a data management plan specific to your project, and provides you with links and resources for ensuring your plan is successful.
Cal Poly - Data Management for ResearchersCarly Strasser
October 17, 2013 @ 1 Robert E. Kennedy Library, Data Studio, California Polytechnic State University.
Researchers rarely learn about good data management practices. Instead we develop our own systems that are often unintelligible to others. In this talk, Strasser, PhD, will focus on the common mistakes that scientists make and how to avoid them. She will provide best practices for data management, which will facilitate data sharing and reuse, and introduce tools you can use.
Funders and publishers have something in common: for better or worse, we have the ability to influence the behavior of researchers. This talk will focus on what both groups can do to improve research now and in the future.
A Big Picture in Research Data ManagementCarole Goble
A personal view of the big picture in Research Data Management, given at GFBio - de.NBI Summer School 2018 Riding the Data Life Cycle! Braunschweig Integrated Centre of Systems Biology (BRICS), 03 - 07 September 2018
A talk I gave at the MMDS workshop June 2014 on the Myria system as well as some of Seung-Hee Bae's work on scalable graph clustering.
https://mmds-data.org/
Tools für das Management von ForschungsdatenHeinz Pampel
Workshop „Wege in die Köpfe“ des DFG-Projekts „EWIG - Entwicklung von Workflowkomponenten für die Langzeitarchivierung von Forschungsdaten in den Geowissenschaften“ | Berlin, 03.07.2014
Data Repositories: Recommendation, Certification and Models for Cost RecoveryAnita de Waard
Talk at NITRD Workshop "Measuring the Impact of Digital Repositories" February 28 – March 1, 2017 https://www.nitrd.gov/nitrdgroups/index.php?title=DigitalRepositories
DataShare - Pauline Ward to University of Edinburgh School of Chemistry - 3 f...University of Edinburgh
Talk targeted at researchers at the University of Edinburgh, explaining how they can use DataShare to publish their research results, and some of the benefits of doing so.
IDCC Workshop: Analysing DMPs to inform research data services: lessons from ...Amanda Whitmire
A workshop as part of the International Digital Curation Conference 2016 on DMP development and support. This presentation demonstrates how we can use data management plans as a source of information to better understand researcher data stewardship practices and how to support them. Be sure to see the slide notes to better understand the presentation (most slides are just photos/icons).
Keynote on software sustainability given at the 2nd Annual Netherlands eScience Symposium, November 2014.
Based on the article
Carole Goble ,
Better Software, Better Research
Issue No.05 - Sept.-Oct. (2014 vol.18)
pp: 4-8
IEEE Computer Society
http://www.computer.org/csdl/mags/ic/2014/05/mic2014050004.pdf
http://doi.ieeecomputersociety.org/10.1109/MIC.2014.88
http://www.software.ac.uk/resources/publications/better-software-better-research
A Presentation on Data Stewardship & Data Advocacy - the Benefits and Advantages of Implementing a Data Strategy for Businesses originally presented to the Directorial Team at Business Link North West and the North West Development Agency
Agencies such as the NSF and NIH require data management plans as part of research proposals and the Office of Science and Technology Policy (OSTP) is requiring federal agencies to develop plans to increase public access to results of federally funded scientific research. These slides explore sustainable data sharing models, including models for sharing restricted-use data. Demos of these models and tips for accessing public data access services are provided as well as resources for creating data management plans for grant applications.
Business Semantics for Data Governance and StewardshipPieter De Leenheer
Data quality and regulations are perpetual drivers for Data Governance and Stewardship solutions that systematically monitor the execution of data policy. And yet, there is a long road ahead to achieve Trust in Data. It is still a relatively unknown topic or comes with trauma from past failed attempts; there is no political framework with executive champions, leading to reactive rather than proactive behavior, and software support is marginal.
Data Governance and Stewardship requires automation of business semantics management at its nucleus, in order to achieve a wide adoption and confluence of Data Trust between business and IT communities in the organization.
In this lecture, we start by reviewing 'C' in ICT and reflect on the dilemma: what is the most important quality of data: truth or trust? We review the wide spectrum of business semantics. We visit the different phases of data pain as a company grows, and we map their situation on this spectrum of semantics.
Next, we introduce the principles and framework for business semantics management to support data governance and stewardship focusing on the structural (what), processual (how) and organizational (who) components. We illustrate with stories from the field.
In that session we will discuss about Data Governance, mainly around that fantastic platform Power BI (but also around on-prem concerns).
How to avoid dataset-hell ? What are the best practices for sharing queries ? Who is the famous Data Steward and what is its role in a department or in the whole company ? How do you choose the right person ?
Keywords : Power Query, Data Management Gateway, Power BI Admin Center, Datastewardship, SharePoint 2013, eDiscovery
Level 200
Data Systems Integration & Business Value Pt. 1: MetadataDATAVERSITY
Certain systems are more data focused than others. Usually their primary focus is on accomplishing integration of disparate data. In these cases, failure is most often attributable to the adoption of a single pillar (silver bullet). The three webinars in the Data Systems Integration and Business Value series are designed to illustrate that good systems development more often depends on at least three DM disciplines (pie wedges) in order to provide a solid foundation.
Much of the discussion of metadata focuses on understanding it and the associated technologies. While these are important, they represent a typical tool/technology focus and this has not achieved significant results to date. A more relevant question when considering pockets of metadata is: Whether to include them in the scope organizational metadata practices. By understanding what it means to include items in the scope of your metadata practices, you can begin to build systems that allow you to practice sophisticated ways to advance their data management and supported business initiatives. After a bit of practice in this manner you can position your organization to better exploit any and all metadata technologies.
Data Stewardship is an approach to Data Governance that formalises accountability for managing information resources on behalf of others and for the best interests of the organization
Data Stewardship consists of the people, organisation, and processes to ensure that the appropriately designated stewards are responsible for the governed data.
RWDG Webinar: Metadata to Support Data GovernanceDATAVERSITY
Metadata is a by-product of executing and enforcing authority over the management of data. Metadata is also a by-product of formalizing accountability for the management of data. It is impossible to deliver a successful Data Governance program without it. Identifying the appropriate metadata and applying the appropriate level of governance around the metadata is a critical success factor.
In this RWDG webinar, Bob Seiner will discuss the relationship between Data Governance success and the management of metadata. Bob will share how to focus on the most important metadata to support your program and the role it plays in the demonstration of value.
This webinar will cover:
•The Relationship between Good Governance and Metadata
•Selecting the First and Right Metadata to Manage
•Using the Metadata to Support Your Program
•Using the Program to Support Your Metadata
•Building Governance Metadata into Everyday Events
Data Stewardship and Governance: how to reach global adoption and systematic ...Pieter De Leenheer
Data quality and regulations are perpetual drivers for Data Governance solutions that systematically monitor the execution of data policy. And yet, there is along road ahead to achieve Data Governance: the term is still relatively unknown, there is no political forum in the form of a Data Governance Council, and software support is moderate. Time for change ! Data Governance requires automation on the one hand and a wide adoption of business to ICT on the other.
In this lecture, we set out the basic principles to successful develop Data Governance. By way of example, we show how to translate this in Collibra's Data Governance Center. We pay particular attention to identifying and modelling data policies and rules, and to empowering them on the basis of data stewardship and configurable workflows across silos and functions in the organization. The example is drawn from the Flanders Research Information Space, where data quality is critical to drive and boost pan-European Research policy.
This presentation was provided by Carly Strasser of the Chan Zuckerberg Initiative during the NISO hot topic virtual conference "Effective Data Management," which was held on September 29, 2021.
Being FAIR: FAIR data and model management SSBSS 2017 Summer SchoolCarole Goble
Lecture 1:
Being FAIR: FAIR data and model management
In recent years we have seen a change in expectations for the management of all the outcomes of research – that is the “assets” of data, models, codes, SOPs, workflows. The “FAIR” (Findable, Accessible, Interoperable, Reusable) Guiding Principles for scientific data management and stewardship [1] have proved to be an effective rallying-cry. Funding agencies expect data (and increasingly software) management retention and access plans. Journals are raising their expectations of the availability of data and codes for pre- and post- publication. The multi-component, multi-disciplinary nature of Systems and Synthetic Biology demands the interlinking and exchange of assets and the systematic recording of metadata for their interpretation.
Our FAIRDOM project (http://www.fair-dom.org) supports Systems Biology research projects with their research data, methods and model management, with an emphasis on standards smuggled in by stealth and sensitivity to asset sharing and credit anxiety. The FAIRDOM Platform has been installed by over 30 labs or projects. Our public, centrally hosted Asset Commons, the FAIRDOMHub.org, supports the outcomes of 50+ projects.
Now established as a grassroots association, FAIRDOM has over 8 years of experience of practical asset sharing and data infrastructure at the researcher coal-face ranging across European programmes (SysMO and ERASysAPP ERANets), national initiatives (Germany's de.NBI and Systems Medicine of the Liver; Norway's Digital Life) and European Research Infrastructures (ISBE) as well as in PI's labs and Centres such as the SynBioChem Centre at Manchester.
In this talk I will show explore how FAIRDOM has been designed to support Systems Biology projects and show examples of its configuration and use. I will also explore the technical and social challenges we face.
I will also refer to European efforts to support public archives for the life sciences. ELIXIR (http:// http://www.elixir-europe.org/) the European Research Infrastructure of 21 national nodes and a hub funded by national agreements to coordinate and sustain key data repositories and archives for the Life Science community, improve access to them and related tools, support training and create a platform for dataset interoperability. As the Head of the ELIXIR-UK Node and co-lead of the ELIXIR Interoperability Platform I will show how this work relates to your projects.
[1] Wilkinson et al, The FAIR Guiding Principles for scientific data management and stewardship Scientific Data 3, doi:10.1038/sdata.2016.18
Data and Donuts: How to write a data management planC. Tobin Magle
This presentation describes best practices for how to write a data management plan for your research data. Additionally, it provides information about finding funder requirements, metadata standards, and repositories.
PIDs, Data and Software: How Libraries Can Support Researchers in an Evolving...Sarah Anna Stewart
Presentation given at the M25 Consortium of Academic Libraries, CPD25 Event on 'The Role of the Library in Supporting Research'. Provides an introduction to data, software and PIDs and a brief look at how libraries can enable researchers to gain impact and credit for their research data and software.
Most of the time, when you hear about Artificial Intelligence (AI), people talk about new algorithms or even the computation power needed to train them. But Data is one of the most important factors in AI.
Responsible conduct of research: Data ManagementC. Tobin Magle
A presentation for the Food and Nutrition Science Responsible conduct of research class on data management best practices. Covers material in the context of writing a data management plan.
Presentation given at the Indiana University School of Medicine's Ruth Lilly Medical Library. Contains information and resources specific to Indiana University Purdue University Indianapolis (IUPUI). For full class materials, see LYD17_IUPUIWorkshop folder here: https://osf.io/r8tht/.
Presentation from a University of York Library workshop on research data management. The workshop provides an introduction to research data management, covering best practice for the successful organisation, storage, documentation, archiving, and sharing of research data.
Workshop - finding and accessing data - Cambridge August 22 2016Fiona Nielsen
Finding and accessing human genomic data for research
University of Cambridge, United Kingdom | Seminar Room G
Monday, 22 August 2016 from 10:00 to 12:00 (BST)
Charlotte, Nadia and Fiona presented an overview of data sources around the world where you can find genomics data for your research and gave examples of the data access application for dbGaP and EGA with specific details relevant for University of Cambridge researchers.
ESA Ignite talk on UC3 Dash platform for data sharingCarly Strasser
Ignite talk (20 slides / 15 seconds per slide) for ESA 2014 meeting in Sacramento, CA 12 August 2014. On the Dash platform for helping researchers manage and share their data via institutional repositories
Data Management for Mountain Observatories WorkshopCarly Strasser
Keynote presentation for 2014 Mountain Observatories Workshop, 16 July 2014.
Abstract:
While methods for collecting data are well taught, there is less emphasis on managing the resulting data effectively. New mandates, announcements, memos, and requirements from agencies and publishers are emerging that encourage better data management, data sharing, and data preservation. Scientists with good management skills will be able to maximize the productivity of their own research, effectively and efficiently share their data with the community, and benefit from the re-use of their data by others. I will offer an overview of data management landscape - discussing recent events, resources, and new directions for data stewardship. I will also cover best practices for data management, which will facilitate data sharing and reuse, and introduce tools researchers can use to help in their data stewardship endeavours.
Libraries & Research Data Management for CO Alliance of Resrch LibrariesCarly Strasser
Keynote presentation for the Colorado Alliance of Research Libraries 2014 Research Data Management Conference, 11 July 2014. Focuses on why data management and sharing is important, and the role of libraries.
Open Science for Australian Institute of Marine Science WorkshopCarly Strasser
*Please excuse the typos :)
Presentation on open science and open data for the Australian Institute of Marine Science (AIMS) workshop on "Raising your research profile using research data". 18 June 2014.
Data management overview and UC3 tools for IASSIST 2014Carly Strasser
Presentation to introduce current landscape of data management and UC3 tools and services that support data sharing. For IASSIST in Toronto, 5 June 2014.
Data Publication for UC Davis Publish or PerishCarly Strasser
Intro presentation for panel on going beyond publishing journal articles. UC Davis "Publish or Perish?" Event, 13 Feb 2014. Sorry about missing gradient on some of slides!
October 18, 2013 @ Kennedy Library, Data Studio, Cal Poly. We hear about all things “open” these days: open access, open source, open data, open science, et cetera. But what does it really mean for how we do science? How are things changing, and what are the implications for individual researchers?
Cal Poly - Data Management: Who knew it was a hot topic?Carly Strasser
October 17, 2013 @ Robert E. Kennedy Library, Data Studio, California Polytechnic State University.
New mandates, announcements, memos, and requirements are emerging that encourage better data management, data sharing, and data preservation. In this presentation, data curation specialist Carly Strasser, PhD, offers a lay of the data management land by discussing recent events, resources, and new directions for data stewardship.
Overview of data management policies and data management plans, including the DMPTool. For Ecological Society of America 2013 Meeting in Minneapolis, MN 5 August 2013.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
20. Because reproducibility* is one of
the fundamental tenets of science.
*reproducibility: being able to go from data to figures/results
not reproducibility: independently verifiable via following same
techniques.
23. Because reproducibility is one of
the fundamental tenets of science.
Because we need to be credible.
Because Fox News, creationism,
and the war on science.
24. “Help us identify grants that are wasteful
or that you don’t think are a good use of
taxpayer dollars.” !
Rep. Adrian Smith (R-Nebraska), a member of the House Committee on Science
and Technology
25. Because reproducibility is one of
the fundamental tenets of science.
Because we need to be credible.
Because Fox News, creationism,
and the war on science
Because it means faster progress.
33. … “Federal agencies investing in research and
development (more than $100 million in annual
expenditures) must have clear and coordinated
policies for increasing public access to
research products.”
Feb
2013
34. 1. Maximize free public access
2. Ensure researchers create data
management plans
3. Allow costs for data preservation and
access in proposal budgets
4. Ensure evaluation of data management
plan merits
5. Ensure researchers comply with their data
management plans
6. Promote data deposition into public
repositories
7. Develop approaches for identification and
attribution of datasets
8. Educate folks about data stewardship
From Flickr by Joe Crimmings Photography
40. Use descriptive file names
• Unique
• Reflect contents
From
R
Cook,
ESA
Best
Practices
Workshop
2010
Bad:
Mydata.xls
2001_data.csv
best version.txt
Better:
Eaffinis_nanaimo_2010_counts.xls
Site
name
Year
What was
measured
Study
organism
*Not for everyone
*
Planning
Design file naming scheme
43. A relational database is
A set of tables
Relationships among the tables
A language to specify & query the tables
A RDB provides
Scalability: millions+ records
Features for sub-setting, querying, sorting
Reduced redundancy & entry errors
From Mark Schildhauer
Planning
Consider a database
44. You should invest time in learning databases if
your data sets are large or complex
Consider investing time in learning databases if
your data are small and humble
you ever intend to share your data
you are < 30 years old
Planning
From Mark Schildhauer
Consider a database
45. Store your data in a repository
Institutional archive
Discipline/specialty archive
Pick a data repository
From Flickr by torkildr
Ask a librarian
Repos of repos:
databib.org
re3data.org
Planning
46. FromFlickrbysepasynod
From Flickr by taberandrew
From Flickr by withassociates
What software?
What hardware?
What personnel?
How often?
Set up reminders!
Test system
Decide on preservation/backup
Planning
47. …document that
describes what you will
do with your data
throughout
the research project
From Flickr by Barbies Land
Write a data
management plan!
Planning
48. DMP components
But they all have
different requirements
and express them in
different ways
• What will be collected
• Methods
• Standards
• Metadata
• Sharing/access
• Long-term storage
Planning
From Flickr by Barbies Land
49. Step-by-step wizard for generating DMP
create | edit | re-use | share
Free & open to community
dmptool.org
Planning
51. Realistically:
• Archive .csv version of raw data
• Make a “raw” tab in working data file
• Do all work on other tabs
During
collection
Keep raw data raw
52. Raw data as .csv
R script for processing & analysis
During
collection
Ideally:
• Use scripts to process data
• Save them with data
Keep raw data raw
53. During
collection
Document your workflow
Temperature
data
Salinity
data
Data import into Excel
Analysis: mean, SD
Graph production
Quality control &
data cleaning
“Clean” T
& S data
Summary
statistics
Data in
spread-
sheet
Workflow: how you get from the raw data to the final
products of your research
Simple workflow: flow chart
54. During
collection
Workflow: how you get from the raw data to the final
products of your research
Simple workflow: commented script
• R, SAS, MATLAB…
• Well-documented code is
Easier to review
Easier to share
Easier to use for repeat analysis
#
%
$
&
Document your workflow
59. Create parameter table
From doi:10.3334/ORNLDAAC/777
From doi:10.3334/ORNLDAAC/777
From R Cook, ESA Best Practices Workshop 2010
During
collection
Break down spreadsheets
Fake a relational database
Create a site table
61. Metadata: data reporting
WHO created the data?
WHAT is the content
of the data set?
WHEN was it created?
WHERE was it collected?
HOW was it developed?
WHY was it developed?
FromFlickrby//ichaelPatric|{
During
collection
Create metadata
62. Digital context
• Name of the data set
• The name(s) of the data file(s) in the
data set
• Date the data set was last modified
• Example data file records for each data
type file
• Pertinent companion files
• List of related or ancillary data sets
• Software (including version number)
used to prepare/read the data set
• Data processing that was performed
Personnel & stakeholders
• Who collected
• Who to contact with questions
• Funders
Scientific context
• Scientific reason why the data were
collected
• What data were collected
• What instruments (including model & serial
number) were used
• Environmental conditions during collection
• Temporal & spatial resolution
• Standards or calibrations used
Information about parameters
• How each was measured or produced
• Units of measure
• Format used in the data set
• Precision & accuracy if known
Information about data
• Definitions of codes used
• Quality assurance & control measures
• Known problems that limit data use (e.g.
uncertainty, sampling problems)
During
collection
Create metadata
63. • Provide structure to describe data
Common terms | definitions | language | structure
• Come in many flavors
EML , FGDC, ISO19115, DarwinCore,…
• Can be met using software tools
Morpho (EML), Metavist (FGDC), NOAA MERMaid (CSGDM)
What is
metadata?
Metadata standards…
During
collection
Standard
<
Create metadata