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Analysis of Biological Networks (BE.440)
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This class analyzes complex biological processes from the molecular, cellular, extracellular, and organ levels of hierarchy. Emphasis is placed on the basic biochemical and biophysical principles that govern these processes. Examples of processes to be studied include chemotaxis, the fixation of nitrogen into organic biological molecules, growth factor and hormone mediated signaling cascades, and signaling cascades leading to cell death in response to DNA damage. In each case, the availability of a resource, or the presence of a stimulus, results in some biochemical pathways being turned on while others are turned off. The course examines the dynamic aspects of these processes and details how biochemical mechanistic themes impinge on molecular/cellular/tissue/organ-level functions. Chemical and quantitative views of the interplay of multiple pathways as biological networks are emphasized. Student work culminates in the preparation of a unique grant application in an area of biological networks.

Subject:
Applied Science
Biology
Engineering
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Essigmann, John
Sasisekharan, Ram
Date Added:
09/01/2004
Analyzing Findings
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By the end of this section, you will be able to:Explain what a correlation coefficient tells us about the relationship between variablesRecognize that correlation does not indicate a cause-and-effect relationship between variablesDiscuss our tendency to look for relationships between variables that do not really existExplain random sampling and assignment of participants into experimental and control groupsDiscuss how experimenter or participant bias could affect the results of an experimentIdentify independent and dependent variables

Subject:
Psychology
Social Science
Material Type:
Module
Author:
Melinda Boland
Date Added:
01/12/2018
Are Psychology Journals Anti-replication? A Snapshot of Editorial Practices
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Recent research in psychology has highlighted a number of replication problems in the discipline, with publication bias – the preference for publishing original and positive results, and a resistance to publishing negative results and replications- identified as one reason for replication failure. However, little empirical research exists to demonstrate that journals explicitly refuse to publish replications. We reviewed the instructions to authors and the published aims of 1151 psychology journals and examined whether they indicated that replications were permitted and accepted. We also examined whether journal practices differed across branches of the discipline, and whether editorial practices differed between low and high impact journals. Thirty three journals (3%) stated in their aims or instructions to authors that they accepted replications. There was no difference between high and low impact journals. The implications of these findings for psychology are discussed.

Subject:
Psychology
Social Science
Material Type:
Reading
Provider:
Frontiers in Psychology
Author:
G. N. Martin
Richard M. Clarke
Date Added:
08/07/2020
Cell Biology: Structure and Functions of the Nucleus
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The goal of this course is to teach both the fundamentals of nuclear cell biology as well as the methodological and experimental approaches upon which they are based. Lectures and class discussions will cover the background and fundamental findings in a particular area of nuclear cell biology. The assigned readings will provide concrete examples of the experimental approaches and logic used to establish these findings. Some examples of topics include genome and systems biology, transcription, and gene expression.

Subject:
Biology
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Sharp, Phillip
Young, Richard
Date Added:
02/01/2010
Conducting Agricultural Research
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Students will explore the steps in conducting scientific investigation in Agriculture and discuss safety precautions that should be followed in conducting agricultural research. Lesson plan from the New Mexico Animal, Plant, and Soil Science Lesson Plan Library.

Subject:
Agriculture
Material Type:
Activity/Lab
Assessment
Diagram/Illustration
Lecture Notes
Lesson Plan
Author:
Owl Nest Manager
Date Added:
01/30/2023
DNA and the end replication problem
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This activity will help students understand how the enzyme telomerase works to solve the "end replication problem."

Subject:
Anatomy/Physiology
Applied Science
Health, Medicine and Nursing
Life Science
Material Type:
Diagram/Illustration
Interactive
Module
Provider:
Oregon State University
Author:
Open Oregon State
Oregon State University
Date Added:
05/18/2021
Deep Dive into Open Scholarship: Collaboration and Replication
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This deep dive session on replications and large-scale collaborations introduces a glossary of relevant terms, the problems these initiatives address, and some tools to get started. Panelists start with content knowledge transfer but switch to more interactive conversation for Q&A and conversation.

Subject:
Education
Material Type:
Lesson
Author:
Erin Miller
Jay Carter
Scott Peters
Matt Makel
Date Added:
03/15/2021
Genetics
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This course discusses the principles of genetics with application to the study of biological function at the level of molecules, cells, and multicellular organisms, including humans. The topics include: structure and function of genes, chromosomes and genomes, biological variation resulting from recombination, mutation, and selection, population genetics, use of genetic methods to analyze protein function, gene regulation and inherited disease.

Subject:
Biology
Genetics
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Fink, Gerald
Kaiser, Chris
Mischke, Michelle
Samson, Leona
Date Added:
09/01/2004
Getting Involved with TOP Factor
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CC BY
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This webinar provides an overview of TOP Factor: its rationale, how it is being used, and how each of the TOP standards relate to individual scores. We also cover how to get involved with TOP Factor by inviting interested community members to suggest journals be added to the database and/or evaluate journal policies for submission.

Subject:
Education
Material Type:
Lecture
Provider:
Center for Open Science
Date Added:
03/21/2021
Implementations are not specifications: Specification, replication and experimentation in computational cognitive modeling
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Contemporary methods of computational cognitive modeling have recently been criticized by Addyman and French (2012) on the grounds that they have not kept up with developments in computer technology and human–computer interaction. They present a manifesto for change according to which, it is argued, modelers should devote more effort to making their models accessible, both to non-modelers (with an appropriate easy-to-use user interface) and modelers alike. We agree that models, like data, should be freely available according to the normal standards of science, but caution against confusing implementations with specifications. Models may embody theories, but they generally also include implementation assumptions. Cognitive modeling methodology needs to be sensitive to this. We argue that specification, replication and experimentation are methodological approaches that can address this issue.

Subject:
Social Science
Material Type:
Primary Source
Author:
Olivia Guest
Richard P. Cooper
Date Added:
11/13/2020
Instead of "playing the game" it is time to change the rules: Registered Reports at AIMS Neuroscience and beyond
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The last ten years have witnessed increasing awareness of questionable research practices (QRPs) in the life sciences, including p-hacking, HARKing, lack of replication, publication bias, low statistical power and lack of data sharing (see Figure 1). Concerns about such behaviours have been raised repeatedly for over half a century but the incentive structure of academia has not changed to address them. Despite the complex motivations that drive academia, many QRPs stem from the simple fact that the incentives which offer success to individual scientists conflict with what is best for science. On the one hand are a set of gold standards that centuries of the scientific method have proven to be crucial for discovery: rigour, reproducibility, and transparency. On the other hand are a set of opposing principles born out of the academic career model: the drive to produce novel and striking results, the importance of confirming prior expectations, and the need to protect research interests from competitors. Within a culture that pressures scientists to produce rather than discover, the outcome is a biased and impoverished science in which most published results are either unconfirmed genuine discoveries or unchallenged fallacies. This observation implies no moral judgement of scientists, who are as much victims of this system as they are perpetrators.

Subject:
Life Science
Psychology
Social Science
Material Type:
Reading
Provider:
AIMS Neuroscience
Author:
Christopher D. Chambers
Eva Feredoes
Peter Etchells
Suresh Daniel Muthukumaraswamy
Date Added:
08/07/2020
Internal conceptual replications do not increase independent replication success
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Recently, many psychological effects have been surprisingly difficult to reproduce. This article asks why, and investigates whether conceptually replicating an effect in the original publication is related to the success of independent, direct replications. Two prominent accounts of low reproducibility make different predictions in this respect. One account suggests that psychological phenomena are dependent on unknown contexts that are not reproduced in independent replication attempts. By this account, internal replications indicate that a finding is more robust and, thus, that it is easier to independently replicate it. An alternative account suggests that researchers employ questionable research practices (QRPs), which increase false positive rates. By this account, the success of internal replications may just be the result of QRPs and, thus, internal replications are not predictive of independent replication success. The data of a large reproducibility project support the QRP account: replicating an effect in the original publication is not related to independent replication success. Additional analyses reveal that internally replicated and internally unreplicated effects are not very different in terms of variables associated with replication success. Moreover, social psychological effects in particular appear to lack any benefit from internal replications. Overall, these results indicate that, in this dataset at least, the influence of QRPs is at the heart of failures to replicate psychological findings, especially in social psychology. Variable, unknown contexts appear to play only a relatively minor role. I recommend practical solutions for how QRPs can be avoided.

Subject:
Psychology
Social Science
Material Type:
Reading
Provider:
Psychonomic Bulletin & Review
Author:
Richard Kunert
Date Added:
08/07/2020
Introduction to Biology
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The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.
7.012 focuses on the exploration of current research in cell biology, immunology, neurobiology, genomics, and molecular medicine.
Acknowledgments
The study materials, problem sets, and quiz materials used during Fall 2004 for 7.012 include contributions from past instructors, teaching assistants, and other members of the MIT Biology Department affiliated with course #7.012. Since the following works have evolved over a period of many years, no single source can be attributed.

Subject:
Biology
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Chess, Andrew
Gardel, Claudette
Lander, Eric
Weinberg, Robert
Date Added:
09/01/2004
Introductory Biology
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The MIT Biology Department core Introductory Biology courses, 7.012, 7.013, 7.014, 7.015, and 7.016 all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. The focus of 7.013 is on genomic approaches to human biology, including neuroscience, development, immunology, tissue repair and stem cells, tissue engineering, and infectious and inherited diseases, including cancer.

Subject:
Biology
Genetics
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Amon, Angelika
Ray, Diviya
Sive, Hazel
Date Added:
02/01/2018
Introductory Biology
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The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.
7.014 focuses on the application of these fundamental principles, toward an understanding of microorganisms as geochemical agents responsible for the evolution and renewal of the biosphere and of their role in human health and disease.
Acknowledgements
The study materials, problem sets, and quiz materials used during Spring 2005 for 7.014 include contributions from past instructors, teaching assistants, and other members of the MIT Biology Department affiliated with course 7.014. Since the following works have evolved over a period of many years, no single source can be attributed.

Subject:
Biology
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Chisholm, Penny
Khodor, Julia
Mischke, Michelle
Walker, Graham
Date Added:
02/01/2005
Introductory Biology
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The MIT Biology Department core courses, 7.012, 7.013, and 7.014, all cover the same core material, which includes the fundamental principles of biochemistry, genetics, molecular biology, and cell biology. 7.013 focuses on the application of the fundamental principles toward an understanding of human biology. Topics include genetics, cell biology, molecular biology, disease (infectious agents, inherited diseases and cancer), developmental biology, neurobiology and evolution.
Biological function at the molecular level is particularly emphasized in all courses and covers the structure and regulation of genes, as well as, the structure and synthesis of proteins, how these molecules are integrated into cells, and how these cells are integrated into multicellular systems and organisms. In addition, each version of the subject has its own distinctive material.

Subject:
Biology
Genetics
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Jacks, Tyler
Sinha, Diviya
Sive, Hazel
Date Added:
02/01/2013
The Meaningfulness of Effect Sizes in Psychological Research: Differences Between Sub-Disciplines and the Impact of Potential Biases
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Effect sizes are the currency of psychological research. They quantify the results of a study to answer the research question and are used to calculate statistical power. The interpretation of effect sizes—when is an effect small, medium, or large?—has been guided by the recommendations Jacob Cohen gave in his pioneering writings starting in 1962: Either compare an effect with the effects found in past research or use certain conventional benchmarks. The present analysis shows that neither of these recommendations is currently applicable. From past publications without pre-registration, 900 effects were randomly drawn and compared with 93 effects from publications with pre-registration, revealing a large difference: Effects from the former (median r = .36) were much larger than effects from the latter (median r = .16). That is, certain biases, such as publication bias or questionable research practices, have caused a dramatic inflation in published effects, making it difficult to compare an actual effect with the real population effects (as these are unknown). In addition, there were very large differences in the mean effects between psychological sub-disciplines and between different study designs, making it impossible to apply any global benchmarks. Many more pre-registered studies are needed in the future to derive a reliable picture of real population effects.

Subject:
Psychology
Social Science
Material Type:
Reading
Provider:
Frontiers in Psychology
Author:
Marcus A. Schwarz
Thomas Schäfer
Date Added:
08/07/2020
Openness and Reproducibility: Insights from a Model-Centric Approach
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This paper investigates the conceptual relationship between openness and reproducibility using a model-centric approach, heavily informed by probability theory and statistics. We first clarify the concepts of reliability, auditability, replicability, and reproducibility–each of which denotes a potential scientific objective. Then we advance a conceptual analysis to delineate the relationship between open scientific practices and these objectives. Using the notion of an idealized experiment, we identify which components of an experiment need to be reported and which need to be repeated to achieve the relevant objective. The model-centric framework we propose aims to contribute precision and clarity to the discussions surrounding the so-called reproducibility crisis.

Subject:
Social Science
Material Type:
Primary Source
Author:
Berna Devezer
Erkan Ozge Buzbas
Luis G. Nardin
Bert Baumgaertner
Date Added:
11/13/2020