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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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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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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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Cold emailing 101: What is it, and how do I start?

What is cold emailing?

So, what is it? Cold emailing is a proactive approach to reaching out to potential employers, researchers, or professionals without any prior relationship or introduction. Most research internships, if not all, aren’t through official programs, are gained through cold emails. Through personalized emails expressing genuine interest in researching a specific field, you can demonstrate initiative and enthusiasm for scientific exploration. Cold emailing enables you to expand your network beyond conventional avenues (i.e. official summer programs), providing an opportunity to showcase your passion for science and your eagerness to contribute. By being genuine and enthusiastic, you can catch open doors to amazing opportunities that otherwise might not be widely advertised.

1. Pick your field(s) of interest

With numerous branches of science offering a wide range of fascinating topics, it can be overwhelming to pinpoint the perfect fit. To begin the journey, start by exploring your academic interests and passions. Reflect on any science courses, videos, movies, or any kind of media that have intrigued you—that you could see yourself truly enjoy studying. Consider the areas in which you felt a natural curiosity to learn more, and write down a list. Identifying these initial interests will serve as a foundation for narrowing down the fields later on.

Once you have a general direction, take a few hours to do some general internet research into the subfields within your chosen science discipline. For example, if you’re interested in biology, explore fields like genetics, ecology, neuroscience, or microbiology. Watch videos, read books, and scroll through articles. Additionally, it can help to take into account the societal relevance and potential impact of the research you are drawn to. Understanding how your chosen field contributes to addressing real-world challenges can add a deeper sense of purpose to your research pursuits. If possible, look for opportunities to attend webinars or workshops that expose you to these domains. If you don’t find yourself actively engaged in the topic and eager to learn more, then it might not be a preferable field and you can cross it off your list. You can end up with more than one interesting fields, and that’s okay!

Next, consider the practical aspects of conducting research in a specific field. Evaluate the resources available, such as research facilities or academic institutions that specialize in your chosen area. If you live near any kind of university, research their departments and see if they offer what you would like to study. Consider the resources and facilities available at each university. Some research projects may require access to specialized equipment, labs, or collaborative opportunities. Ensure that the universities you are considering can provide the necessary resources to support your research interests. Make sure to keep in mind transportation to and from the potential lab, as well as your time availability.

Remember that choosing a field of science to research is a dynamic and evolving process, and it’s essential to find a balance between what captivates your curiosity and what aligns with your long-term career aspirations.

2. Make a list of desired professors

Once you have your field(s) of interest and facility location(s) chosen, now it’s time to start making a list of possible researchers you’d want to work under.

Delve into the faculty profiles of the universities you are considering. Most researchers are either professors or associate professors at a university. Look for professors whose research aligns closely with your own interests. Oftentimes the professors will have a link to their lab website in their faculty profile, which will have much more detailed information. Pay attention to their publications, ongoing projects, and areas of expertise. Take note of any professors whose work resonates with you, and create a list of potential mentors.

It’s also beneficial to attend academic conferences, seminars, or webinars in your field, if possible. Although this definitely isn’t required, these events offer opportunities to connect with professors, ask questions, and learn more about their research and mentoring philosophy. Networking with professionals in your field can provide valuable insights and may even lead to further potential research opportunities.

As you compile your list of desired professors, prioritize them based on your level of interest and fit with your research goals. Having multiple professors from the same university department is totally okay, but it’s also beneficial to aim to have a diverse list of potential mentors, including professors from different institutions and research backgrounds. Keep in mind that crafting this list is a dynamic process, and your preferences may evolve as you gain more exposure to the research community.

3. Curate your resume

Curating and customizing your resume for a research position at a university lab is essential to showcase your academic qualifications, research experience, and passion for scientific inquiry. Start by creating a clear and concise resume that highlights your academic achievements, relevant coursework, and any research-related experiences you have had so far. Include your education, major, and any honors or awards you have received that demonstrate your dedication to academic excellence. If you haven’t had any prior research experience or notable awards, don’t worry! Some labs may require previous experience or qualifications, but most of the time they are just as open (if not more) to budding scientists. The PIs are usually professors—they teach students, and you’re here to learn!

If you do have experience, tailor your resume to emphasize research-related skills and experiences. If you have participated in any research projects or internships, describe them in detail, highlighting the methodologies used, data analysis techniques, and any notable findings or contributions. If you have presented your research at conferences or published any papers, be sure to include these accomplishments.

Include a section dedicated to technical skills that are relevant to the research position you are applying for. This might include laboratory techniques, software proficiency, or any specialized equipment you have experience using. Demonstrating your technical expertise will show potential mentors that you are well-prepared to contribute to their research team.

4. draft an email outline

Drafting a cold email outline for getting a research internship requires a structured and engaging approach to capture the attention of potential mentors. Start with a concise and professional subject line that clearly states your intention. Mentioning “Research Internship Inquiry” or something similar will immediately convey the purpose of your email.

In the opening paragraph, introduce yourself briefly, providing your name, age, and academic background. This should not be the bulk of your email, and should only be a few (if not one) sentences long

The second paragraph should express your enthusiasm and passion for the specific area of research you are interested in. Be specific! Explain what specific area you’re interested in, why you’re interested in it, and why this professor’s work aligns with your interests. It’s imperative you tailor your email to the specific research interests of the professor or lab you are reaching out to. Mention any publications or ongoing projects from the lab that have caught your attention and explain why their work aligns with your interests, which will show that you’ve done your research and are genuinely interested in contributing to their research team. This is arguably the most important part of the email, because it demonstrates your interest and proactivity. Professors can easily tell if you did your research on them or not based on what you say you’re interested in. (e.g., if you were to write to a professor researching protein synthesis about your passion for immunology, they will be able to tell you didn’t do your research thoroughly enough).

Next, describe your research experiences, if you have any. Describe any previous research projects, internships, or lab work you have been involved in, even if they weren’t related to your current potential field. This paragraph does not have to be long—a few sentences will do. Take a brief sentence afterwards to mention that you’re resume is attached, should they want to know more.

In the closing paragraph, express your eagerness to join their research team as an unpaid volunteer or intern. It might be trickier to explicitly say intern depending on which lab you’re emailing, as paid researchers are usually paid through grants and they might not be able to allocate enough funds for you. Request the opportunity to discuss the internship further, either online (like a phone call or video conference) or in person. Offer to provide any additional information they may need, such as sample works or publications.

Lastly, end your email with a professional and polite closing, such as “Thank you for considering my application” or “I look forward to the possibility of working with you.” Be sure to include your contact information, including your email address and phone number, so that they can easily get in touch with you.

Here’s an example template:

Subject: Research Internship Inquiry

Dear [Professor’s Name],

I hope this email finds you well! My name is [Your Name], and I am a [your academic year] at [your university/institution].

Throughout my academic journey, I have developed a strong interest in [specific research area of interest]. I was particularly intrigued by your work on [mention a specific project or publication from the professor’s lab], because [how the project aligns with your interests].

I have previously studied [mention any previous research projects, internships, or lab work you’ve been involved in]. It was an amazing opportunity, and I greatly enjoyed learning about [relevant knowledge you’ve gained], including learning and gaining experience in a variety of lab experiences from [list relevant techniques or methodologies you are proficient in] to [list other relevant techniques or methodologies you are proficient in].

I am impressed by the collaborative and intellectually stimulating environment of your lab, and I believe that working under your mentorship would provide me with invaluable learning opportunities. As an enthusiastic and dedicated individual, I am committed to contributing my best efforts to support ongoing projects and address research questions with rigor and creativity.

I am writing to inquire if there may be a possibility for me to participate in research activities in your lab, perhaps as a volunteer or unpaid intern. I am keen to contribute in any way and broaden my experience in [specific research area of interest]. I am open to arrange a meeting, phone call, or video conference at your convenience should you be interested.

My resume is attached for your review and I welcome any questions you may have.

Thank you for considering my application, and I look forward to your response.

Best regards,

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

6. Extra tips

1. send multiple emails / have backups

Sending cold emails to multiple professors is crucial to increase your chances of receiving a response and securing a research internship. Because the research landscape is competitive, professors receive numerous emails from interested students, and not all emails may be immediately noticed or responded to. By reaching out to multiple professors, you expand the pool of potential opportunities and increase the likelihood of finding a match with a research mentor who has availability and is interested in your academic background and research interests. While one professor may have limited availability for interns, another might be actively seeking motivated students to join their research team.

However, do NOT copy and paste each email to each professor. Although some professor’s area of research may be extremely similar, no two professors are studying the same exact area. You must tailor each email to each professor and their work in the lab in order to show them that you are invested in their work and not their colleague’s work.

2. Humble brag, but don’t be too cocky

If you have previous experience or projects that align with your interest, don’t be afraid to talk about them! Your email and resume are the only chance you get to tell them about your accomplishments. Take care to talk in a neutral tone, and avoid sounding too conceited. Though professors will definitely be looking at your past accomplishments, they are also looking to see who you are as a person. They take into account your personality and collaborative potential, making it really important to show them how your traits align with what they look for.

Best of luck!

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Navigating conferences and symposiums: tips for attending and presenting

Research conferences and symposiums bring together scientists, researchers, and scholars from diverse fields to share knowledge, present findings, and foster collaborations. Research conferences are larger events covering a broad range of topics with multiple presentations and diverse attendees. Symposia, on the other hand, are specialized, focused events with shorter durations, emphasizing in-depth discussions on a specific theme and attracting attendees with keen interest in that topic. Both provide valuable opportunities for knowledge exchange and networking among researchers and experts.

Presenting at a symposium can be an exciting and rewarding experience, offering an opportunity to showcase your research and receive valuable feedback. In this comprehensive guide, we’ll cover what to expect, how to prepare, essential oral presentation tips, and tricks to make your symposium presentation a success.

Understand the Symposium Format:

Familiarize yourself with the symposium’s structure, including the duration of your presentation, Q&A session, and any specific guidelines or themes set by the organizers. In a conference, you’ll usually be given a set duration of time. For a symposium, you are generally standing in front of your poster, and other people will come and ask questions.

Preparation is key:

  • Begin your preparation well in advance to have ample time for refining your content and polishing your delivery. Organize your thoughts, data, and key messages to create a coherent and impactful presentation. You generally will not have notes during your presentation, so make sure you fully understand your material before presenting.
  • Focus on conveying a clear and concise message. Structure your presentation logically, with a strong introduction, well-defined objectives, main findings, and a compelling conclusion.
  • Use visual aids like slides, graphs, and images to enhance your presentation and make complex concepts easier to understand. Keep the design clean, consistent, and avoid clutter.
  • Rehearse your presentation multiple times to become familiar with the content and improve your delivery. Practice in front of friends or colleagues to receive feedback. Remember to stay mindful of the allocated presentation time. Practice delivering your talk within the time limit to avoid rushing or exceeding the allotted time. For symposia, it’s generally good to have a few-minute elevator pitch.

Presenting:

  • Tailor your presentation to the symposium’s audience, which may include fellow researchers, scholars, students, and industry professionals. Adjust your language and level of technical detail accordingly.
  • Anticipate potential questions and prepare concise and accurate responses. Be open to feedback and engage in constructive discussions during the Q&A session.
  • Summarize your key points and reiterate the importance of your research. Leave a lasting impression by offering avenues for future research or applications.
A peek of one of our writer’s own symposium!

Other tips:

  • Networking Opportunities
    Take advantage of networking opportunities during breaks and social events to connect with other presenters, experts, and potential collaborators.
  • Enjoy the Experience:
    Remember that presenting at a symposium is a valuable opportunity to share your work and contribute to your field. Embrace the experience with enthusiasm and passion!

Goodluck!

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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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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.