Tag: clinical research

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Conducting bioinformatics research

Regardless of whether you’re an experienced researcher or a newcomer to this field, this comprehensive guide will walk you through the vital steps for conducting bioinformatics research effectively.

Step 1: Define Your Research Objectives

At the outset of your bioinformatics research journey, it is imperative to establish clear research objectives. Begin by formulating the scientific questions you aim to answer. What questions do you want to answer? What are you looking to solve? What problems are you looking to address? Articulate your specific research objectives and the outcomes you anticipate achieving.

Step 2: Acquire Relevant Skills and Knowledge

Gain an in-depth understanding of biology, encompassing the biological systems and processes pertinent to your research. Familiarize yourself with genetic concepts and genome sequencing techniques, which form the bedrock of many bioinformatics projects. Delve into computer science, where mastering programming languages such as Python and R is indispensable. Additionally, acquire proficiency in data analysis and familiarize yourself with a diverse array of bioinformatics tools.

Step 3: Access Data Resources

One of the foundational components of bioinformatics research involves working with biological data. To access pertinent data resources:

Rely on databases such as GenBank, NCBI, and Ensembl, each offering extensive repositories of genetic and genomic data. Explore data repositories provided by institutions like the European Bioinformatics Institute (EBI) or the National Center for Biotechnology Information (NCBI) (guide on how to navigate these sites coming soon!).

Step 4: Select Appropriate Tools and Software

Selecting the right tools and software is imperative for successful bioinformatics research. Opt for tools and software that align with your research requirements: Bioconductor is an invaluable resource for genomics data analysis in R. Biopython provides a comprehensive toolkit for computational biology in Python. BLAST, a widely-used tool, facilitates sequence similarity searches. Tailor your choice of phylogenetics software, whether it be MEGA, RAxML, or BEAST, to the specific demands of your research.

Step 5: Data Collection and Preprocessing

Gather the data needed for your research and prepare it for analysis: Initiate the process by meticulously cleaning and formatting your data. Subsequently, expunge duplicates, contaminants, or sequences of inferior quality to ensure data integrity. Normalize data, if required, to achieve consistency in your dataset.

Step 6: Data Analysis and Visualization

Data analysis is the core of bioinformatics research and encompasses several crucial components:

Embark on your data analysis journey by deploying descriptive statistics to gain a comprehensive understanding of your dataset. Apply relevant algorithms such as sequence alignment, sequence assembly, or clustering, depending on the objectives of your research. You might want to do some further research into each of these analyses and which one suits your personal project. Enhance your research by visualizing your results through plots, graphs, and interactive tools that facilitate comprehension.

Step 7: Interpret and Draw Conclusions

Interpretation of research findings is essential in bioinformatics research: Thoroughly analyze your results in the context of your research objectives, ensuring they are in alignment. Frame meaningful conclusions and hypotheses based on your findings. Discuss the implications and significance of your research, emphasizing how it contributes to the broader understanding of your research domain.

Step 8: Document Your Work

Comprehensive documentation is pivotal to the success of your bioinformatics research:

Maintain a research notebook to meticulously record your progress, insights, and observations. Utilize version control for both code and data to keep an organized and traceable record of your research. Document data sources, analysis methods, and results thoroughly to ensure reproducibility and transparency in your work.

Step 9: Seek Funding and Resources

Bioinformatics research often demands computational resources and support. Explore opportunities to secure funding:

Look into grants, scholarships, and funding opportunities tailored to your research area. Seek access to high-performance computing clusters or cloud computing resources to facilitate your computational needs.

Goodluck!

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informationals

Field vs. Laboratory Research

Research is the cornerstone of expanding our knowledge and understanding of the world around us.

Field research is the collection of raw data outside a laboratory, library, or workplace setting. It aims to capture the authenticity of real-world interactions, making it particularly suitable for studying social behaviors, ecological systems, and cultural dynamics. Researchers gather data through methods like observations, surveys, interviews, participant observation, and ethnography. This approach provides a holistic perspective on the studied phenomena, shedding light on various involved factors and enabling exploration within their natural settings.

On the other hand, lab research takes place within controlled laboratory environments. This controlled setting enables researchers to manipulate variables precisely and systematically, facilitating the establishment of cause-and-effect relationships. Controlled experiments, simulations, and controlled observations are commonly employed in lab research. This approach is well-suited for isolating specific variables, making precise measurements, and conducting experiments with a focus on internal validity.

The advantages of field research

Field research comes with notable advantages. It allows researchers to observe phenomena in their natural complexity, capturing interactions that might be difficult to replicate in a lab setting (ex. archaeology, sociology, any kind of cultural or social construct, etc.). The findings often possess high ecological validity, making them applicable to real-world situations. Yet field research has its own limitations. The lack of control over external factors can introduce confounding variables, and the process can be resource-intensive and time-consuming due to logistical challenges. It can be hard to isolate singular phenomena when there are dozens of other factors accounted for but not managed.

The advantages of lab research

The strength in lab research is in its ability to control variables and minimize external influences, resulting in enhanced internal validity. Replicating experiments is relatively straightforward, increasing the confidence in the findings. Factors are accounted for and controlled, allowing for the elimination of most confounding variables. Nonetheless, lab research has its own set of limitations. Controlled environments might oversimplify the complexities of real-world phenomena, potentially leading to demand characteristics or a lack of ecological validity. Sometimes these confounding variables are integral for the phenomena to happen, and without these variables at play, the experiment itself may be oversimplified. Moreover, some phenomena, particularly those deeply embedded in natural contexts, cannot be accurately studied in lab settings.

What kind of research am I doing for my project?

Determining the appropriate approach depends on the research objectives, the nature of the studied phenomena, available resources, and ethical considerations. Field research shines when exploring intricate social interactions, studying ecosystems, and investigating cultural phenomena. Meanwhile, lab research is valuable for establishing causal relationships and isolating variables under controlled conditions.

In practice, researchers often blend these approaches to maximize their insights. Field observations can inform the design of lab experiments, while lab findings can be tested and validated in real-world scenarios.

Considering cost and resources, field research often demands more due to travel, equipment, and logistical requirements. On the other hand, lab research can be cost-effective in terms of equipment and personnel, but it might involve significant initial setup.

Validity and reliability are key considerations. Field research prioritizes external validity and naturalistic settings, possibly at the expense of internal validity. In contrast, lab research emphasizes internal validity while potentially sacrificing ecological validity.

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how to

How to find the right research field for you

Begin by exploring your academic strengths and curiosities. Take note of the subjects or courses that excite you the most and consider how they might relate to research topics. If you liked your biology class, consider exploring biology subtopics such as genetics, immunology, virology, and more. If you liked your math class, consider researching topics in pure mathematics, applied mathematics, or even computer science. Reflect on the activities or projects that have sparked your curiosity outside of the classroom, as they can provide valuable clues about your interests.

Engaging with extracurricular opportunities, such as science clubs, STEM competitions, or science fairs, can expose you to a wide array of scientific disciplines. High school Olympiads (SciOly, BioOly, USACO, etc.) are great examples of this. Participating in these activities allows you to gain hands-on experiences, work on collaborative projects, and interact with mentors and professionals in various fields. This exposure will help you discover areas that captivate your imagination and inspire a desire to delve deeper into specific research questions.

Additionally, reading scientific articles, books, or attending lectures and talks on different scientific topics can broaden your knowledge and give you insights into various research fields. Pay attention to how you feel while exploring different subjects – genuine excitement and curiosity often indicate that a research field may be a good fit for you.

Moreover, consider seeking guidance from teachers, mentors, or professionals in the field. They can provide valuable advice, share their experiences, and help you connect with research opportunities that align with your interests. Consider seeking out teachers in your favorite class and asking about their experience. What do they like about their subject? What do they not? What have they done in the field so far? Don’t hesitate to reach out to experts or researchers in areas you find intriguing; their insights can be invaluable in shaping your research journey.

Ultimately, finding the research field that best suits you involves exploration, curiosity, and a willingness to try new things. Embrace the process of discovery and stay open to new possibilities. Remember that your interests may evolve over time, and it’s okay to explore multiple research fields before settling on the one that truly resonates with you. By following your passion and engaging in various research experiences, you will pave the way to a fulfilling and rewarding research path.

Here is a list of possible topics you can consider (please keep in mind that there are vast amounts of different fields and topics to go into, so don’t limit yourself to these):

  • Computer science / Artificial Intelligence (AI): AI involves the development of computer systems that can perform tasks that typically require human intelligence, such as speech recognition, problem-solving, and decision-making.
  • Environmental science / climate change: The study of climate change focuses on understanding the long-term shifts in Earth’s climate patterns and the impact of human activities on the environment.
  • Biology / Cancer Research: This field seeks to uncover the underlying causes of cancer, develop innovative treatments, and improve early detection methods to combat this complex disease.
  • Neuroscience: Neuroscience investigates the structure and function of the nervous system to understand brain development, behavior, cognition, and neurological disorders.
  • Genomics: Genomics involves the study of an organism’s entire DNA sequence to uncover genetic variations, understand heredity, and improve personalized medicine.
  • Quantum Computing: Quantum computing explores the principles of quantum mechanics to develop powerful computers capable of solving complex problems at unprecedented speeds.
  • Bioinformatics: Bioinformatics combines biology, computer science, and mathematics to analyze and interpret biological data, such as DNA sequences and protein structures.
  • Stem Cell Research: Stem cell research investigates the potential of these versatile cells to regenerate and repair damaged tissues, leading to breakthroughs in regenerative medicine.
  • Computer science / Cybersecurity: Cybersecurity aims to safeguard digital information and systems from cyberattacks and data breaches, protecting individuals, organizations, and governments.
  • Nanotechnology: Nanotechnology involves manipulating materials at the nanoscale to create new materials, devices, and applications with unique properties.
  • Computer science / Machine Learning: Machine learning explores algorithms and statistical models that enable computers to learn from and improve their performance on specific tasks without explicit programming.
  • Virology: This field investigates the causes, transmission, and treatment of infectious diseases, such as HIV, malaria, and COVID-19.
  • Biotechnology: Biotechnology applies biological principles to create new products, therapies, and technologies for medicine, agriculture, and industry.
  • Urban Planning: Urban planning studies address the design and development of cities, focusing on infrastructure, transportation, and sustainable growth.
  • Materials Science: Materials science investigates the properties, structure, and applications of various materials, leading to advances in engineering and technology.
  • Pharmacology: Drug discovery research aims to identify and develop new medications to treat various diseases and improve overall healthcare.
  • Behavioral Economics: Behavioral economics studies the psychological and emotional factors that influence decision-making, guiding policies and interventions to shape economic behavior.
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guides

Cold emailing 102: I’ve sent the email, now what?

Now, you wait for their response. Cold emailing will often have a very low response rate, so it’s best to stay patient and see who responds.

After a few days of waiting and there’s still no response, here’s what you can do.

1. No response – following up

If your professors still haven’t responded after 1.5-2 weeks, then you can send a follow up email. Sending a follow-up email is essential because it demonstrates your continued interest and shows that you value the opportunity and are committed to the lab. Note that follow ups are generally on the shorter side and much more concise.

Here’s an example template:

Dear [Professor’s Name],

I hope this email finds you well! I remain enthusiastic about the possibility of contributing to your ongoing research projects, and would like to follow up on my previous email regarding a position at your lab.

I wanted to take this opportunity to reiterate my interest in joining your research team. I am eager to immerse myself in the research environment of your lab and apply my skills in [mention any relevant techniques or methodologies you possess]. I am more than willing to provide any additional information you may require, such as references or further details on my research experiences.

Thank you for your consideration, and I hope to have the opportunity to discuss my potential contribution to your lab in person or through a virtual meeting.

Best regards,

[Your Name] [Your Contact Information – Email Address, Phone Number]

2. Followed up, no response – now what?

If after another 1-2 weeks or so and you still haven’t gotten a response, then leave it be. It’s best not to send more than one or two—professors do check their email, and if they haven’t responded after your initial email and a follow up, then chances are they’re not interested.

In the meantime, take the time to do more research and email other professors. Consider applying for official university-affiliated programs or reaching out to other connections around you (including on social media).

Best of luck!

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informationals

Common laboratory terminology

If you’re starting lab research for the first time, or engaging in any science-related discussion, you’re going to hear a lot of words and phrases thrown around that you might not know. Here’s a list of common terms and phrases so you don’t have to ask later on!

  • Primary Investigator: the primary investigator, or PI, is the holder the lab’s research grant and the lead researcher for the grant project. You can think of this person as the boss of the lab or the head researcher.
  • Journal Publication: a scholarly publication containing articles written by researchers, professors and other experts. These are often published only a few times a year, and are the ultimate goal for any researchers. You’ll often hear someone go, “I’m going to be published in XYZ journal!” which means that their research project was published in that journal. Some journals are more prestigious than others, which is determined by their impact factor.
  • Assay: an investigative or analytic procedure for assessing or measuring the presence, amount, or functional activity of a drug. It’s used in a lot of laboratory settings, and can mostly be interchangeable with “experiment”.
  • Lab meeting: exactly what it sounds. Most, if not all, labs hold a weekly lab meeting, where all the people working in the lab will meet and one person will present updates on their work, usually in a form of PowerPoint presentation, and the rest of the lab will ask questions and discuss. The people presenting will rotate each week.
  • Journal club: All labs will also most likely have a journal club, where lab members will take turns each week choosing a scientific paper related to their field of work and present them in a meeting with the rest of the lab members.
  • Peer review: A type of research evaluation, used before a paper is published. Once a paper is submitted to a journal, the journal will have experts in the same field as the author review the paper for any mistakes or fallacies. This ensures the quality and validity of the research.
  • Methodology: The detailed description of the procedures, techniques, and materials used in a research study. It allows other researchers to replicate the experiment.
  • Literature Review: A comprehensive overview of existing research and publications relevant to a specific topic. This helps researchers understand the context of their work and identify gaps in knowledge.
  • Abstract: A concise summary of a research paper, typically located at the beginning. It provides an overview of the study’s objectives, methods, results, and conclusions. Usually around 300 words.
  • Protocol: A standardized procedure or set of guidelines for conducting experiments or research. This is pretty similar to methodology. Protocols ensure consistency and accuracy in data collection and analysis.
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informationals

What is research?

Team of experienced biologists working on microscopes in laboratory

What is research?

Research is the systematic and methodical investigation of a particular topic or issue to generate new knowledge, explore hypotheses, or solve problems. Any kind of research involves a rigorous process of data collection, analysis, and interpretation, often guided by a set of well-defined objectives and questions. Researchers aim to contribute to the existing body of knowledge, make evidence-based discoveries, and drive innovation in diverse fields, from science and technology to social sciences and humanities: a critical component of advancing human understanding and improving various aspects of society.

Different Types of Research:

There are various types of research, each serving unique purposes and applying specific methodologies. Two primary types of research are clinical and translational research.

Clinical Research: Clinical research is conducted to study human health and disease, involving human participants. This type of research typically includes clinical trials to test new treatments, interventions, or medical devices for their safety and effectiveness. Clinical research is vital for developing and improving healthcare practices, understanding disease mechanisms, and identifying potential therapies.

Clinical research opportunities are often much more limited for high school students, as clinical studies and trials require patient interaction, which involves strict rules and regulations.

Translational Research: Translational, also known as bench or wet lab, research bridges the gap between basic scientific discoveries and their practical applications in healthcare settings. It aims to translate scientific findings in the lab into tangible benefits for patients and the broader community. Translational research often involves moving scientific knowledge from the laboratory into clinical trials and eventually integrating the discoveries into medical practice.

Research mentors:

Research mentors play a pivotal role in shaping the success and growth of aspiring researchers. A mentor is an experienced individual, often a senior researcher or faculty member, who provides guidance and expertise to mentees as they embark on their research journey. One of the primary roles of a research mentor is to help the mentee identify their research interests and goals. Mentors also assist in the formulation of research questions and hypotheses, helping mentees refine their research ideas into feasible and well-defined projects. They offer critical feedback on research proposals and guide students in designing robust experimental methodologies or study protocols. Furthermore, mentors introduce mentees to networking opportunities and professional development activities. They may suggest attending conferences, workshops, or seminars to expand the mentees’ exposure to the broader research community and help them build valuable connections with other researchers.

Publication

The culmination of a research project (or any important finding) often leads to publications, where researchers write an article describing their experimentation and findings and publish in an academic journal. Before research findings are published, they undergo a peer review process. In this process, independent experts in the field critically evaluate the research methodology, data analysis, and interpretation to ensure the study’s validity and quality.