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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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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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guides

Applying to summer research programs: high school edition

What are high school research programs?

A high school summer research program is a unique opportunity for students to engage in hands-on research and exploration within their chosen academic fields. These programs are typically offered by universities, research institutions, and organizations. Summer programs are usually co-ed, residential programs that range anywhere from 6-8 weeks and often culminate in a final project or presentation. Participating in a summer research program demonstrates a student’s commitment to academic excellence and passion for their chosen field, making it a valuable addition to college applications. It can significantly enhance the chances of being accepted to competitive colleges and universities while offering a transformative experience that sets students apart from their peers. As exciting summer research programs as a high school student can be, most respected programs are often very competitive (think <10% acceptance rate). Here’s a guide on how to craft the best program application:

To start, most programs require the following:

  • Grades transcript
  • Test Scores
  • Letters of recommendation
  • Supplementary essays / personal statement
  1. Research Available Programs: Look for summer research programs at universities, research institutions, and organizations. Utilize online resources, directories, and databases that specifically cater to high school students seeking research opportunities.
  2. Check Eligibility Criteria: Each program will have specific eligibility requirements, such as grade level, age range, coursework completed, and GPA. Make sure you meet all the prerequisites before proceeding with the application.
  3. Start Early: Begin your search for summer research programs well in advance. Many applications have deadlines several months before the start of the program, so give yourself enough time to research and prepare. Most summer programs open their applications at the end of the year (Oct-Nov) and are due at the beginning of next year (Jan-Feb).
  4. Prepare Your Resume/CV: Create a well-organized resume that highlights your academic achievements, extracurricular activities, volunteer work, leadership experiences, and any previous research-related involvement. Some programs will ask for a resume, and some won’t. Make sure you know which programs ask and don’t ask to save time.
  5. Request Recommendation Letters: Many programs require letters of recommendation from teachers, mentors, or community leaders. Ask for letters from individuals who can speak to your academic abilities, research potential, and enthusiasm for learning.
  6. Write a Stellar Personal Statement: Craft a compelling personal statement that showcases your passion for the subject, explains why you want to participate in the program, and demonstrates your suitability as a candidate. Tailor your statement for each program you apply to. For those that ask for supplementary essays, make sure you start drafting and writing a few months before the deadline.
  7. Check for Financial Assistance: Some summer research programs may come with associated costs. If they do, they will also most likely offer financial aid or scholarships, so make sure to research what they offer.
  8. Submit Your Application: Complete the application accurately and submit all required documents before the deadline. Double-check that all materials, including transcripts, recommendation letters, and essays, are included.

Extra tips:

  1. Stay Organized: Keep track of the programs you’ve applied to, their deadlines, and any communication with program coordinators. An organized approach will help you manage the process effectively.
  2. Consider Backup Options: Apply to multiple programs to increase your chances of acceptance. Have a few backup options ready in case you’re not accepted to your first-choice program.
  3. Prepare for the Program: If you get accepted, familiarize yourself with the program’s schedule, requirements, and any preparations you need to make before the start date.
  4. Make the Most of the Experience: During the program, actively engage in research, ask questions, seek mentorship, and network with peers. Embrace the learning opportunities and make the most of the experience.
  5. Follow Up and Express Gratitude: After the program concludes, send thank-you notes to mentors, program coordinators, and anyone else who contributed to your experience. Networking and expressing appreciation can lead to future opportunities.
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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.