Category: hard research life

Down and out in research and academia. The sometimes funny, sometimes sad stories in a researches life.

Mendeley Advisor of the Month: June 2018

Rachel Brennesholtz

Mendeley advisor of the month: Waris Ali Khan, PhD Scholar in Business Management, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia

Waris Ali Khan comes from the small town of Kasur (Punjab, Pakistan). Currently, he is pursuing a Ph.D. in Business Management from Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia as a full time PhD Scholar. Waris is a founder of WarSha Intellectual Consultancy based in Malaysia (offering academic services to scholars). Moreover, he is extremely dependent on Mendeley as a research tool.

How did you get into your field and what is your research story?

Learning about business and commerce is one of my key targets. I studied commerce since college as I was very clear about my field of interest and gained a Bachelor of Commerce and then went on to gain an MBA. However, my PhD journey started in 2015. I was lucky enough to get a scholarship from the Universiti Malaysia Sabah.  Fortunately, due to one of my friend’s recommendations, I signed up for Mendeley. Since that day, I love to do my work/research using Mendeley as it keeps every single article of mine in a very well managed state. I have heard that people find research very difficult. Maybe they are right, but I think they have probably never used Mendeley.

Where do you do your research/work the best? What kind of environment suits you?

I like to do my job in a relaxed, creative environment with people who also have the same interest for Business.

How long have you been on Mendeley? 

Since, 2016. Luckily one of my friends from India recommended it. Thanks Mr. Ken.

What were you using prior to Mendeley and how does Mendeley influence your research?

The inbuilt MS Word References tool. Mendeley boosted my research by allowing me to annotate and quickly save papers to a place where I can easily retrieve them anytime and anywhere.

It’s also made a huge difference in terms of creation of my citation and bibliography as well – this used to be such a headache and wasted a lot of time but now no more headaches with Mendeley.

Why did you decide to become an Advisor and how are you involved with the program?

I decided to become an advisor because of my ever-increasing interest in the tool to the point of using it quite easily. I thought, why not show it to others? Perhaps they will benefit from the features as I do. From then, I asked Mendeley and was accepted. It made me very happy. Since I became a Mendeley Advisor, I have organized

number of workshops in Malaysia and Pakistan.

What researcher would you like to work with or meet, dead or alive?

I would love to meet the team who developed the SmartPLS software for data analysis as it’s very useful and important for PhD scholars specifically in social science.

 What book are you reading at the moment and why?

I read several books at once related to my PhD work, and many, many scientific papers as well. But I like books related to scientific research method. However, currently I am reading Research Methods for Business (Seventh Edition) by Uma Sekaran and Roger Bougie.

 What’s the most interesting thing you’ve learned this week?

Recently, I was assisting my wife, who is also a PhD scholar at  Universiti Malaysia Sabah in chemical engineering. So, I learned how to do extraction of plants and their analysis using different instruments like HPLC. I was happy to learn about it as it is totally different from my field.

 What is the best part about working in research?

The best part is the opportunity to travel and contact people around the world that, no matter the language, religion, race, etc., share passion and enthusiasm! I am excited about my upcoming conference in Singapore. I hope I will be able to meet with other experienced researchers.

 And the worst/most challenging part about working in research?

The most challenging is to overcome the challenges of publication in scientific journals of high impact. Competition is very strong and there are other influences besides the scientific merit that one not should mention. But the joys are greater still.

 What is the one thing you want people to know about Mendeley?

I am quite sure if one uses Mendeley then he/she is going to handover his/her many headaches to Mendeley and, of course for Mendeley, it’s a Mickey Mouse job to deal with your research headaches. Mendeley is the key permitting to open the door to discover the existing research world, no matter the topic you are interested in.

Mendeley Advisor of the Month: May 2018

contentstrategymedia

Mendeley advisor of the month: Dr Jordan Steel, Assistant Professor Cell Biology, Molecular Virology, Colorado State University.

Colorado State University-Pueblo faculty member Dr. Jordan Steel received the 2017 National Association of Biology Teachers (NABT) Four-Year College & University Biology Teaching Award for his highly innovative project- and team-based learning approach to his courses. A native of Albuquerque, NM, he has lived in Colorado since 2008 and enjoys spending time with his family hiking, biking, fishing, playing games, and going on adventures together to discover the amazing world we live in.

How did you get into your field and what is your research story?

I have always been interested in microbiology and have been fascinated with the molecular basis of life. From 2005-2007, I lived in the Philippines and experienced first-hand the devastation caused by mosquito-borne viral infections. Upon returning to the US, I applied and started graduate school at Colorado State University’s Arthropod-borne Infectious Disease Lab (AIDL) to study viral pathogens such as Dengue virus and West Nile Virus. My Ph.D. dissertation worked primarily with alphaviruses and modifying the viral genome to develop reporter systems within cell lines and genetically modified mosquitoes to enhance our detection of viral infection. Near the end of my Ph.D., I worked on a project on how viral infection induces oxidative stress during infection. I fell in love with this project and later moved on to a Postdoc position to study viral manipulation of host cell metabolic pathways during Dengue virus infection. I am now an assistant professor and have my own research group and we are actively working to understand how viruses modify cellular physiology in order to create an optimal environment for viral replication.

Where do you do your research/work the best? What kind of environment suits you?

Away from home! (I have 4 kids at home and I always joke around with my colleagues that I can’t get any work done at home).  Honestly, I work well in fast-paced environments with lots going on.  I enjoy the thrill and the pressure of working with lots of projects and trying to keep on top of all the demands. It can be hectic and busy, but the productivity that comes from groups with lots happening is very exciting.

How long have you been on Mendeley? 

I can’t remember the date exactly, but I can remember how it has changed my life. It was probably 2011 or 2012 and I was working to finish my Ph.D., I was unhappy with the other citation/reference managing software available and then a friend showed me Mendeley and it has changed my life! I use it almost every day since then!

What were you using prior to Mendeley and how does Mendeley influence your research?

I was using Endnote before I found Mendeley, but now I am a convert and advocate for everything Mendeley! Mendeley is the one-stop shop for all things research. It manages all of my references, allows easy annotations, helps me quickly find papers and notes from the past, and even finds and suggest articles that I should be reading! I love it!

Why did you decide to become an Advisor and how are you involved with the program?

I actually contacted Mendeley and asked to be an advisor. I teach lots of classes in our biology department and one of the first things I teach in my courses is about Mendeley. Every student and person working in biological sciences needs to know about Mendeley. I asked Mendeley if I could become an advisor and help share the good news about Mendeley and they were kind enough to accept me.

What researcher would you like to work with or meet, dead or alive?

So many great people to choose from, but I would love to meet Jonas Salk- the developer of the poliovirus vaccine. As a virologist myself, I have always been impressed and fascinated with his work and commitment to the research that he was doing! He even injected the vaccine on himself before it was fully approved. His work has saved millions of lives and it would be an honor to meet and talk virology with him.

What book are you reading at the moment and why?

Harry Potter and the Chamber of Secrets (remember that I have 4 kids at home), other than that I have been reading my Mendelian Genetics textbook because I am teaching genetics this semester and, well, it has been a long time since I took a genetics class.

What’s the most interesting thing you’ve learned this week?

From reading my genetics textbook- Laron Syndrome is an autosomal recessive disorder that results in a short individual (due to a mutated growth hormone receptor) and also makes them resistant to certain types of cancer and diabetes.

What is the best part about working in research?

I love that each day is something different. We are always working on new problems and new questions. I also love the quality of people that I get to work with. I have decided that scientists are the best kind of people. I love my colleagues and the always changing research environment.

And the worst/most challenging part of working in research?

Funding. No explanation needed.

What is the one thing you want people to know about Mendeley?

Mendeley is the best. It is literally the answer to all of your problems and will make your life easier and better immediately. Everyone needs to know about Mendeley and use it in their research endeavors!

The INQUA Project is bringing researchers together – across disciplines, across Europe.

Sarah E Hoey

INQA

The research environment is changing rapidly, with an ever increasing focus on interdisciplinary collaborations. Often this means collaborators are in different countries, which further complicates the process of team work and communication. Today’s guest blog post is from Dr Erick Robinson (Ghent University, Belgium), who is part of the INQUA Project 1404. The primary aim of this project is to bring together young researchers experts within Europe to investigate the variable impacts of gradual versus abrupt palaeoenvironmental change on human cultural change. Dr Robinison’s post provides a summary of the project’s objective and requirements as well as it’s challenges and how they are overcoming those obstacles.

The long windows of time offered by data from the palaeosciences (archaeology, geology, physical geography, palaeoclimatology, palaeoecology) are essential to our understanding of the potential impacts of future climate and environmental changes on ecosystems and humans throughout the world. Over the last decade, interdisciplinary research in the palaeosciences has started to advance tremendously our knowledge of the shear complexities of past climate and environmental changes, and the diversity of ecosystem and human responses to these changes. These advances have included an awareness of a range of different climate and environmental changes with variable causes, durations, and magnitudes: gradual ecosystem changes in species composition, sea-level rise, abrupt climate changes caused by glacial meltwater outbursts, and extreme events such as tsunamis and volcanic eruptions. The short windows of time traditionally taken into account in modelling the potential impacts of future climate changes therefore risks a lack of knowledge regarding the relationships between environmental changes of different temporal durations and geographical scales of impact. It is imperative that future research considers these longer windows of time in order to understand the broader complexity and dynamics of environmental changes throughout human history.Robinson Riede Mendeley blog entry 1

Caption: An example of how cultural and environmental records can be studied in tandem. This figure shows a comparison of revised radiocarbon chronology for the Early and Middle Mesolithic in the Rhine-Meuse-Scheldt area of northwest Europe (G-I) (calculated with OxCal 3) with selected climate records of the Northern Hemisphere that indicate multiple Early Holocene cooling events (A-F). A: timing of Ice-rafted debris peaks (Bond et al., 1997) indicating the frequency of sea-ice; Greenland (NGRIP) ice core δ18O record (Rasmussen et al., 2006) with GICC05 timescale calibrated into years relative to AD 1950, a temperature proxy; c: Greenland ice core (GISP2) K+ record (Mayewski et al., 1997), a proxy for atmospheric circulation and wind; d: Oxygen-isotope ratios of precipitation (δ18Op) inferred from deep-lake ostracods from the Ammersee (southern Germany) (von Grafenstein et al., 1999); e: Dongge Cave (China) stalagmite D4 δ18O record (Dykoski et al., 2005) providing information on past temperature; f: Hawes Water (UK) core HWLC1 δ18Oc record based on samples of authigenic calcite indicating temperature. The dark line represents the centennial-scale trend calculated omitting the abrupt cooling events (Marshall et al., 2007). The periods of the 9.3 cal. BP and 8.2 cal. BP cooling events are shaded blue (adapted from Robinson et al., Journal of Archaeological Science, 2013)

Extending the temporal scope of research to consider the relationships between millennial scale, centennial scale, and very abrupt climate and environmental changes across the period of the Last Glacial-Early Holocene (14,000-8,000 years ago) requires ‘big data’ approaches enabling the integration of regional datasets at the continental scale. The International Union for Quaternary Research (INQUA) Commission for Humans and the Biosphere (HaBCom) has recently funded an international research project aiming to integrate archaeological and palaeoenvironmental data across Europe for this important period in Earth and human history. This project (INQUA project) “Cultural and palaeoenvironmental changes in Late Glacial to Middle Holocene Europe—gradual or sudden?” is comprised of a majority of Early Career Researchers across the continent interested in exploring new frontiers in international interdisciplinary research. The project requires published data from all regions of Europe for the time period of focus to be integrated into a database that can be utilized for implementing a range of different computational modelling approaches. Big data research of this nature is challenging for many reasons, possibly the most important of which is specialists in one particular discipline or region integrating, interpreting and utilizing data from another discipline/region. Communication is therefore paramount in data quality assessment and research quality control. The Ph.D., Early Career Researchers, and Senior Researchers in the project are faced with the challenge of maintaining regular communication over the data that is integrated into the database, its employment in different modelling approaches, and the assessment of modelling outputs.

We are very happy to be partnering with Mendeley in facing these challenges in this new generation of international interdisciplinary palaeoscience research. Mendeley Team package provides the perfect collaborative workspace for integrating publications with useful data for the database that we aim to build in this project. Our research network is only able to meet once a year for an annual workshop, therefore Mendeley provides the central nexus of communication during the critical periods of data integration and modelling. The progress of the project will be determined by what our research network collaborators can contribute to the project amidst their busy schedules at their home institutions. We are excited to start this challenging and potentially very fruitful research project with the support of Mendeley.

We are delighted to be working with the Project1404 team, and to be able to support their team collaboration.

You can follow this projects updates through the Twitter hashtag #project1404 and find out more about Team plans here.

 

Free access to Science Direct for early career researchers

Shruti Desai1 Comment

Research is not always a linear path, especially in a market squeezed by shrinking grant availability, changing job paths, and fewer permanent career positions.

Compounding the issue for early career researchers between positions is the lack of access to resources like current and archived research.

Elsevier is seeking to alleviate the pressures for between-jobs researchers by continuing a program to help early career researchers who are between positions stay up-to-date on their respective fields. The Postdoc Free Access Program grants complimentary access to books and journals on ScienceDirect for up to six months.

More details from Elsevier:

Post-Doc Free Access Programme: Back by popular demand.

Stay current in your field–even in an uncertain job market

In November 2012 and again in June 2013 we launched a programme to support young scholars in between jobs or looking for their first postdoctoral position. Applicants who qualified were granted up to 6 months free access to all our journals and books on ScienceDirect and able to use this access to work on grant applications and research project.

We were delighted with the response we got from the community; both from post-doctoral organisations who forwarded the application form link and from researchers who qualified for the free access.

One of the recipients of the 2012 program, Daniele Vergara of the University of Salento in Italy, wrote: “As a postdoc fellow in biological sciences, this program [gave] me the chance to maintain a vital scientific network, to read papers and write grants. In the absence of help from government and local institutions, the Elsevier program was a great experience, an innovative way to support postdocs during their research career.”

As the international economic situation continues to be challenging for scientists starting their career, we have decided to bring back this program. In order to give even more people the option to apply we have extended the application period to 7 months.

How to get the Free Access Passport

To qualify, candidates must complete a form verifying their credentials by September 30, 2014. Once approved, they will receive a personal code allowing access to ScienceDirect.

Qualifying criteria are:

  • Postdoctoral researchers who have received their PhD within in the past five years.

  • Candidates must have completed the last research position (either PhD research or a postdoc or equivalent) on or after January 1, 2014, or have a position that will end before October 1, 2014.

Applicants should submit a scanned image of a letter from their last academic mentor or advisor that states the position held and the date on which the position ended or will end. For more on the program and an application, visit elsevier.com/postdocfreeaccess

If you take part in this program, or did last year, share your stories with us! We would love to hear from you.

 

An organized folder is a sign of a… file organizer

Ricardo Vidal17 Comments

As a PhD student I find myself roaming the Internet quite a bit in search of literature for my research project which can be really time consuming. Looking for the right keywords, opening each relevant result into a new tab, downloading each paper of interest, finding the cryptically named PDF file and then adding it to your library in an organized fashion (phew). So anything that can cut back this strain of accessing and organizing research papers is most welcome.

In previous posts I’ve mentioned Mendeley’s web importer, which helps retrieve papers directly to your Mendeley Web account. That’s all good, but what about papers that you already have on your computer spread about in different folders or hard drives?

There are multiple ways to import files from your hard drive directly into Mendeley Desktop. You can add one file at a time, a full folder in one go or even make a specific “Watched” folder.

A “Watched” folder is basically a folder that Mendeley keeps an eye on for any new files and automatically imports new documents with minimal interaction on your behalf. Just drop or download your PDF documents into your watched folder and Mendeley will do it’s thing (I mean auto-extract it’s metadata and add it to your library!).

So we now have a web importer for online retrieval and an automated watch folder. Looks like we are set!

My references and documents are all nice and organized within Mendeley Desktop and accessible online but when I look at the files on my computer, I notice something. In fact, I notice the lack of something: meaningful file names.

Filename Mystery

As you can see in the image above, the file names are not very explanatory and whenever I have to pick a file to send to a colleague or open it directly for some reason, it becomes a guess-the-mystery-file name game. Not to mention that every time I add a file to that folder with a similar name, I get this fantastic message:

The file you are trying to copy “sdarticle.pdf” already exists. Cancel or overwrite?

Good question, do I want to overwrite sdarticle.pdf? Do I have any idea what is in that file? The most probable answer to both these questions is no. Once again, Mendeley has considered this situation and provides an effortless way to organize your files with a built-in feature called: ‘File Organizer’.

As the name suggests, this feature can organize your files for you in a few different ways. You can store your files in a centralized folder with all the files renamed to a specific format. The format is easy to customize by simply dragging the naming categories from one input box to the other.

File Organizer

As you can see in the image above, I chose to rename my files and keep them in one folder with the file name following the format Author – Year – Title. I did not add the journal to the file name, but could have easily done so by just dragging it down into the file name.

There’s an option to organize the files into sub-folders, however I chose not to do so. That’s just my personal choice even though I know colleagues of mine prefer to separate things into sub-folders by year.

Once I’ve picked how I want my files to be sorted and renamed, I go ahead and click apply. Folders get created, files get renamed and I’m done:

Renamed Filenames

These file names are much easier to understand and are categorised how I want them. This feature has not only organized my files into a folder with proper file names, but it will keep any new documents I add in the same orderly fashion. Neat huh?

Mendeley on a Digital Mission to Texas

Mendeley

Great news! We’ve been picked by Chinwag and the UKTI to don our cowboy boots and Stetson hat before jetting off to the great Lone Star State on a Digital Mission.

“39 of the UK’s leading digital companies have been selected for the second annual Digital Mission to South by South West interactive (SXSWi), taking place in Austin, Texas from 11-17th March 2010. […] The successful companies were chosen from over 120 submissions by an advisory board of industry experts drawn from the UK community including: VC’s, export specialists, journalists and industry pundits to take part in the Digital Mission to SXSWi.”

(You can find the full list of participating companies here.)

There are some great presentations in the line-up at SXSWi, some of the ones we’ll be looking out for include: Can the Real-Time Web be Realized?; Crowd Sourcing Innovative Social Change and Is The Brain The Ultimate Computer Interface?

Digital Mission Union JackWe also hope to swot up on doing business in the US (not by watching re-runs of Dallas) but attending some special events and seminars set up for tech entrepreneurs. SXSWi brings together some of the brightest minds in the tech world and a line up of special programs showcasing websites, video games and start-up ideas. If you are planning to attend, let us know and we’ll be happy to hook up.

A big thanks to Digital Mission for making it possible and we’re looking forward to a great event!

Where did Mendeley go?

Andi Rutherford

Happy Thanksgiving: Around 5pm yesterday Mendeley services ceased when all of our servers went offline simultaneously; we quickly realised that something was very wrong with our connection to them and this was confirmed by our hosting provider’s customer service calling us to let us know.

Twitter - Victor @ Mendeley- What are the odds

The details are not completely clear at the moment however we do know that the data centre suffered a very serious power outage, and it appears that there were some faults with their back-up generator and batteries too. In summary, we didn’t have much influence: our servers were stuck in the data centre without power, unreachable for around 2 hours, due to issues sadly outside of our control.

After we re-established contact, the process of checking data integrity, restoring backups as necessary, and testing the system took us another 8 hours – although some of us were up much longer doing their very best to ensure everything was back to normal. Well done Ben and Fred – excellent work! I hope you’re having a well deserved lie-in…

Please be aware that if you were syncing your data around 17:12 UTC yesterday then it would be worth checking everything is ok and contacting support if you are having any problems.

As we are growing in size, we continuously work on scaling Mendeley further. However, yesterday’s combination of events borders on the absurd, and if it were a Mr Bean movie, it would have been funny.

Our apologies that Mendeley was away for so long – we will surely have a word with our data center providers…Normal service has now resumed. Enjoy!

Websense is blocking access to Mendeley… dictators around the globe rejoice

victorhenning2 Comments

Today a user told us that Websense, the internet censorship “content-control” software, websensehas marked the Mendeley website as “Illegal or Questionable” and blocked access to it. I wonder how that happened?

At least we’re in good company. Websense is blocking access to Amnesty International in many parts of the world (wait… now it makes sense! I’m a member of Amnesty!), and has also been blocking GMail and the MIT website just because they can.

Also, I think their logo exhibits a slightly flawed sense of humour. Yes?

An excellent EuroScience adventure, Part I

victorhenning4 Comments

Well, what can I say! The EuroScience Open Forum 2008 in Barcelona has turned out great so far. Due to its considerable greatitude and excellent greatishness, Jan decided not to let me have all the fun by myself and joined me yesterday.

On the downside, the heat and travel stress didn’t exactly help me get rid of my still-persisting cough/throat inflammation. I was barely able to sleep again for the first two nights in Barcelona, and I will need some more days rest at home when I return to London. Nonetheless, we attended some very inspiring sessions and received enthusiastic feedback on our presentation today (more on that in a later post) – let me recapitulate.

Saturday, the most interesting session was on “Open Science” or “Open Notebook Science”, on which Prof. Peter Murray-Rust from Cambridge gave a very spirited talk…

…followed by a not-so-spirited talk given by he-who-shall-not-be-named and in which every slide looked like this:

Anyhow, “Open Notebook Science” is a fairly recent idea which has gained more and more exposure in the past few months. The basic premise is that researchers should not only share their publications through Open Access outlets, but also freely publish their raw data alongside it so that it can be validated, re-purposed and aggregated.

This, of course, entails some problems: Academic careers and tenure decisions depend on publications, so how can you incentivise researchers to lay open their data before they’re certain that they have “wrung” all possible publications out of it? I believe that our “Last.fm for research” model, i.e. the chart-like tracking of which papers are being widely read, which authors are up-and-coming etc., could also be extended to raw data – thus giving credit to people who have created the raw data that others are successfully using.

Two other highlights yesterday and today were the keynote speeches by Prof. Marcus du Sautoy from Oxford and by Physiology/Medicine Nobel laureate Dr. Richard J. Roberts. Both described how they had discovered their love of science and the fields they wanted to dedicate themselves to. Little known facts:

Prof. du Sautoy originally wanted to become a spy (to get a nice black gun like his mum, who had worked for the foreign office) and thus tried to learn many different languages. By his own admission, he failed miserably because he did not find languages to be logical enough. Fortunately for him, Mathematics – and especially Symmetry, his field of expertise – offered him a way of describing and understanding the world in more logical terms. Finally, despite his obsession with symmetry, he had this wonderful quote from the 14th-century Japanese Essays in Idleness:

In everything […] uniformity is undesirable. Leaving something incomplete makes it interesting, and gives one the feeling that there is room for growth… Even when building the imperial palace, they always leave one place unfinished.

This reminded me strikingly of the Law of Closure in Gestalt psychology which describes how the mind will try to complete figures if they are unfinished – hence deliberately leaving something incomplete will engage the mind’s creativity.

Today, then, Dr. Roberts spoke about his way from unruly, almost-expelled-from-school teenager to molecular biologist and Nobel laureate.

Dr. Roberts had actually wanted to become a professional snooker player – back in the 1960s, he was West England snooker champion. That was also when he received what he described as one of his most profound life lessons:

During a snooker tournament, he had sunk an incredible “lucky shot” – but then failed to make the next one. After the game, an old man came down from the audience and said to him:

Listen, if you sink a lucky shot like that, you have to concentrate twice as hard on your next shot. Everyone can be lucky, but if you get lucky – don’t feel bad, instead work extra hard to take advantage of it.

Seems to have worked out alright for him! After the talk, I hopped onto the stage to give Dr. Roberts a brief pitch of Mendeley, since he’s now actively involved in the Open Access movement. I’m sure that he gets loads of requests like these, but if we’re lucky, who knows – he might just find our idea interesting enough to give us some feedback.

Finally, here are two pictures of me wearing a brain helmet, looking at my brain activity (and oddly, not seeing any?!):

Phew. I should stop writing now. Must sleep. Will tell more of our exploits later. Adios!