Your Lab Notebook Goes Digital!

Even though labs today have high-profile technical equipment and produce data mainly digitally, most of the documentation is still done on paper. Labfolder provides an electronic, web-based note book that allows you to store, organize, and analyze your scientific data in a digital format, accessible anytime and anywhere. We met with one of the founders, Florian Hauer.

What is the idea behind Labfolder?
Labfolder is a digital platform where scientists can capture, validate, collect, and also connect all the data and data sources in the laboratory. In most laboratories, scientists still use paper-based lab books. Labfolder transforms these labs into the laboratories of the future, where everything is digital and connected. The idea is that science will be better, more transparent, more reproducible, and more successful if the lab goes digital.

When did you start working on Labfolder?
I started working on Labfolder together with my co-founder Simon Bungers in 2011. It all started with writing a grant for the EXIST fellowship from the German government which awarded us 100.000 EUR to start. We started building the first prototype in 2012 and founded the company in autumn 2013.

You came directly from working in a lab and created Labfolder. What is your background?
My background is molecular biology and biophysics. I had done electron microscopy before I started with Labfolder; it is a discipline which is very data-heavy.

STAYING IN ACADEMIC RESEARCH IS AS RISKY AS FOUNDING A STARTUP

How did you get into this field? Why did you decide not to follow research?
It was curiosity. And then followed by possibility. My co-founder and I were curious to see what it would look like to have our own company. When we got the possibility to do it, we grabbed it immediately. We were often asked if this was not very risky, but our statement is that staying in academic research is equally risky. There is actually no difference whether you want to pursue the academic path, go to the industry or build a startup.

Did you have any training which prepared you for your adventure?
We had to learn everything right in the moment: how to do tax declarations, set up contracts, register a company, and so forth. Luckily, we were embedded in a network from the FU Berlin, which came with our funding. They gave us support in many ways. But I can tell you this: If you have done scientific lab work, then doing the bureaucratic efforts of founding a company is really not rocket science. For a scientist, I would say, it is not a big problem to figure out how to do all these things that are necessary to start and run a company.

What were the milestones in the development and growth of Labfolder?

Our first important milestone was the release of the alpha version in 2012. After only 3 months of development, we released the first very basic prototype of Labfolder, which was already good enough to ignite the interest of some users here at the Charité. More milestones were the steps of publishing new features and available languages. Among the milestones are also the partnerships that we made both with other startups like Mendeley and investors, but also our agreement with the Max Planck society, and very recently with the BIH to roll out Labfolder here at the Charité and the MDC.

FOUNDING A COMPANY IS REALLY NOT ROCKET SCIENCE

 

Who is using Labfolder already and how many customers do you have?
Around 14.000 scientists are using Labfolder. Most are from Germany, but also from the rest of Europe, the US, and Asia. Our customers are 60% academic research laboratories, the others are companies. However, the number of customers does not necessarily reflect the number of users, as for example the Max Planck society is one customer with many users. We also have customers that are using Labfolder in analysis labs with routine testing.

Andrea Claes (l) and Florian Hauer (r) from Labfolder, Photo: Claudia Willmes

How is Labfolder going to evolve in the coming years?
Very soon we will release a few features that will allow scientists to manage their data even better. One feature will allow you to control the experimental parameters in a more structured way, and run queries on your experimental data. Another feature will allow you to link all the material you are using by introducing a material database.
In the long run, we are interested in implementing all the features that allow scientists to get a better grip on their data and make more out of it. The promise of digitalization is not only to have everything digital, but to also do something with the data: To make connections that were there but were not visible before. In the age of big data, it is important to make it possible for scientists to easily store and access it.

What do you like the most about your job?
I like that I have to do something new every day. It never gets boring. There are no normal work days!

What are some of the challenges of your job?
Well, the challenges are also that there is something new every day. But I think it is the challenges that make us grow stronger. I would say that it is probably not the easiest of all jobs, but in our team we are all equally hungry for challenges and for the success that comes with mastering them.

Do you sometimes wish you would be doing experiments in a lab?
I actually still do lab work as a guest scientist! It is very important to me to stay connected to the laboratory and science. Of course, I do much less. I usually take 2 weeks holiday per year which I spend in the lab. I have never lost the connection to the lab and I also plan to keep that in the future.

IN TIMES OF BIG DATA IT'S IMPORTANT TO EASILY STORE AND ACCESS DATA

 
To what extent can Labfolder contribute to better “scientific practice” and data availability?
Labfolder makes it easier to follow the guidelines of good scientific practice, as it is just done automatically without you needing to do anything. Today the main problem of science is that the data are just not accessible to others. If you write up your thesis, you finish your lab notebook and put it on the shelf in your lab: And the data are practically gone! With Labfolder, we want to make sure that future generations of scientists and also the general public will be able to follow your experiments and make use of your data. What ends up in the paper is maybe 5% of the data you have generated, and the rest is lost. It is our mission to provide the technical possibility to share the data in an easy way, and not to share only the tip of the iceberg which is the paper, but also the hidden bottom. These data could be used by others to come to new conclusions and to combine different datasets in order to find new things. With the digital platform for scientific data, there are going to be a lot of possibilities to exchange data. Funding agencies such as the DFG want scientists to share their data, including the raw data. There is a trend to open science and we would like to offer a platform where this trend can become reality.

LABFOLDER IS AN IMPROVEMENT OF  DATA SAFETY AND SECURITY

What about data security? Would it be possible to hack the Labfolder data?
This is a very valid question, but there is no system in the world that is 100% safe. Your paper notebook is also not safe. If you look at large industrial companies that fell victim to espionage, the port of entry never has been the system, but a corrupted person. The risk to be attacked by a hacker is especially high if you have your data on your personal computer or unsecured hard drive. Having your data on Labfolder, where the communication is encrypted and data are stored behind a firewall means security is a lot higher. Also, the Labfolder servers regularly undergo scheduled backups. Even if your computer bursts into flames, your data is still safe in Labfolder. Compared to the many other ways of data storage, Labfolder is actually quiet an improvement of safety and security.

What can our readers do if they want to start using Labfolder?
Using Labfolder at the Charité is now possible! You are very much invited to contact us, either me or Andrea Claes. Andrea will help finding the right strategy to transition from paper based lab book to Labfolder to make it seamlessly easy to jump into the digital lab notebook.

Thank you very much for this interview, we are looking forward to the new features of Labfolder!

This interview was edited for length and clarity
 
Interview by Claudia Willmes, PhD Alumna AG Eickholt / AG Schmitz
This interview originally appeared June 2017 in  CNS Volume 10 - Issue 2

You are very much invited to contact Andrea Claes,
Project & Account Manager, and contact partner for the BIH andrea.claes@labfolder.com

Follow Up: Child/Family Space at Charité

On November 1, 1848 the first US women's medical school opens in Boston. Since then the rights for women changed a lot: In our society it is common that women can study and be doctors just like men. However, as nature can not be changed, it is still the woman who has to carry the baby and breastfeed. Unfortunately this can be an obstacle when a mother-to-be or a breastfeeding mum want to combine motherhood an work.


In our March edition of the newsletter (Vol. 10, Issue 1), we included a series of interviews with female members of the Charité research community. One of our participants mentioned the lack of a room in the CCO for breastfeeding women, or staff members who need a room to rest during their pregnancy (read the full interview here).
Kimberly Mason from the NeuroCure office pointed out that such a room equipped with a couch or mattress for anyone needing a rest was initially planned. Unfortunately, when the Charité highrise renovations began, the CCO had to absorb several groups and services. There was an intense scramble for space and the resting room got repurposed.

However, such a space does actually exist: on Campus Mitte you find it in Hufelandweg 9, Level K1, Room 006. There is also a parent-child room on the Virchow Campus. For details see: https://familienbuero.charite.de/charite_mit_kind/kinderbetreuung/kinderzimmer/

Since one room does not cover the needs of all pregnant women and parents with their children for the whole campus, maybe there is something we can do. We want to explore creative alternatives and would like to hear your opinion.

Thank you Kimberly for the helpful information!

by Claudia Willmes, Post-doc AG Schmitz

This article originally appeared September 2017 in CNS Volume 10, Issue 3, Spirituality in Science

How Wearing a Fitness Tracker Can Change You

Lately, a big market for fitness trackers has emerged. Different wearables and apps can measure a number of fitness-related parameters, including heart rate, GPS tracking, steps, distance covered, pace, calories burned or even sleep quality. In many cases, you can also log your caloric intake to get an even better profile of your performance. But the psychological aspect of fitness trackers is just as important as the technology behind them because they do more than inform: they reinforce, motivate and reward.

The Advertised Effects
Fitness trackers and apps are advertised as beneficial for your health and lifestyle. They provide an objective measure of your activity so you can’t lie to yourself. Wearable trackers should get you to be more active, motivate you during exercise and provide information about your daily routine or workout without requiring manual calculations or notes. Furthermore, they should help you to reach your fitness goals.
These devices and apps are becoming increasingly popular in personal healthcare and promise easy lifestyle changes. These promising words fall on fertile soil. Most adults are aware of (or at least suspect) not meeting their recommended daily activity guidelines. However, there are no objective research results to bolster up their promise of improving physical activity levels.

Do They Work?
Fitness trackers are great for those who really have no idea how many calories they burn during an activity and can help those in need of a motivational tool to keep them going. However, one study found that using a pedometer did not significantly increase step count among overweight and obese adults [1]. Another study with overweight people showed that after 18 months, those who had used a device that tracked steps and calorie expenditure lost on average five pounds less than people without self-tracking [2]. Thus, devices that monitor and provide feedback on physical activity may not offer an advantage over standard behavioral weight-loss approaches after all.

A FITNESS TRACKER INITIALLY INCREASES MOTIVATION

 

From personal observations and a (non-representative) survey among colleagues, it became apparent that a fitness tracker motivated us to be more active initially . For nearly all it was fun to log and track our own health data and progress with colorful charts and badges for achievements. However, the excitement – as with all new toys – had died away at some point and most of us were back to our previous activity levels after a while. Until now, not a single long-term study has analyzed the effect of constantly wearing a fitness tracker on the average consumer.

The Author's Personal Records

What Else Do They Do?
However, many users also observed that they developed a guilty conscience if they had not moved enough. In some cases this led to abandoning the device altogether. Thus, wearing the device alone is not enough to lead a healthier life. Many devices and apps offer an online platform where users can compare themselves with others or even challenge a friend. This additionally increases the motivation, but also the pressure to perform and reach your goals as the wearer is held accountable by the device, app and group members. The motivation to be at the top of a ranking can also be amplified by the ability to broadcast your exercise statistics via social media.

USING A FITNESS TRACKER CAN WORSEN EATING DISORDERS

This can, for obvious reasons, also have negative consequences for some people. One study examined the relationship between use of calorie counting and fitness tracking devices with eating disorder-related behaviour in college students [3]. Participants using calorie and fitness trackers manifested higher levels of eating concern and dietary restraint. Interestingly, fitness tracking, but not calorie counting, emerged as a unique indicator of eating disorder symptomatology. These findings suggest that for some individuals, these devices do more harm than good.

Should I Track?
It is nice to know your daily step count, heart rate, caloric intake, and the like, but wouldn’t you also have an approximate idea about these parameters if you simply reflected on your daily routine? Depending on how important it is for you to know the exact parameters, it makes sense to wear such a device... or not. Many devices have a built-in alarm that goes off if you have not move for a certain time. This might come in handy, but can also be annoying if you are at work and just can’t go for a walk right now. In the end, it always depends on the individual who wears the device.
If you are not prone to being overly critical about your weight, tracking your workouts and food intake can be motivating. But tracking everything might become obsessive for some, as the numerical focus of the trackers is akin to the obsessive fixation characteristic for eating disorders and exercise addiction.
It's true that these devices make you be more aware of your health. However, this can also be achieved without fitness trackers but instead with good education about lifestyle and health.

[1] Takahashi et al, Clin Interv Aging. 2016
[2] Jakicic et al, JAMA. 2016 
[3] Simpson et al, Eat Behav. 2017

by Claudia Willmes, PhD Alumni AG Eickholt/Schmitz

this article originally appeared June 2017 in CNS Volume 10, Issue 2, Digital Health and Big Data  

DeepMind - Will Transparency Make Us Healthier?

You might have heard of DeepMind last year, when they invented a program that could beat human players in the game Go. The British artificial intelligence company, now owned by Google, has been pushing the boundaries of algorithmic learning research for some time now. I was interested to learn that currently their main field of application is healthcare. An entire division of the company is working on a range of challenges with medical data, from interpreting medical images to integrating patient data, all under the banner of DeepMind Health [1].

This work has been taking place in collaboration with a number of UK NHS foundation trusts. For example, a project aimed at detecting and predicting ocular degeneration from digital eye scans is the outcome of a collaboration with Moorfields Eye Hospital London, who have granted access to their database of anonymized digital images of the eye. Similarly, patient CT and MRI scans from University College London Hospital are being used in a machine learning approach to improve treatment planning for head and neck cancers.

How Big Data Helps Medical Professionals
Their largest project has been a collaboration with the Royal Free London NHS foundation trust and Imperial College Healthcare NHS trust in developing a mobile app to provide real-time patient information to nurses and clinicians. Called Streams, this app intends to speed up communication and decision making in hospital environments by replacing a number of older solutions relying on papers, fax, or pagers. The intention is to consolidate a patient’s medical results within a single interface where data-driven alerts can be sent out as soon as there is any indication of a problem, and actions can be decided upon by relevant health workers. The current focus is on a specific disorder, acute kidney injury, where such an approach is presumed to be particularly promising, but obviously the vision extends far more broadly.

Image via pixabay

From this technology, it is not difficult to imagine a future where data from multiple continuous bio-monitoring sources could be integrated so that patients, or any individuals, could be diagnosed and monitored in real-time. Glimpses of this path can already be seen with existing technology like continuous glucose monitoring devices, which provide continuous real-time blood-glucose measurements to diabetics, the data from which can then be accessed (and sometimes shared) via mobile apps [2]. Perhaps even more seemingly mundane biological data could be insightful from a medical perspective - think what information a Fitbit might reveal if state-of-the-art machine learning were applied to its data. Integrating all of these varied sources of information together to generate a comprehensive and detailed medical picture of an individual is surely something DeepMind Health have thought about as well.

DEEPMIND HAVE TAKEN A TRANSPARENCY APPROACH

This whole idea rests upon the ability for a private company to access potentially sensitive patient medical data, and DeepMind were doing just this, often without patient consent. Predictably, this drew some criticism. DeepMind responded earlier this year in an interesting way. Rather than attempting to seek patient consent, they instead took an approach of transparency by announcing their development of a data-logging process - the verifiable data audit.

Transparency vs. Data Privacy
The idea is that a record of all interactions with patient data will be generated and saved, with a log of who was accessing an element of data, when, and for what reason. This record will be automatically updated and stored in a semi-decentralized manner that has been likened to blockchain, with records in a distributed network of healthcare institutions such as hospitals. The data is structured so that any time it is accessed or changed this will be immediately recorded. As such, guidelines can be put in place to ensure that the data isn’t used in unauthorized ways. It also means that all access of data will be traceable forever in a way that should be tamper-proof.
At the epicenter of all this technological innovation is data - as the 21st century is starting to teach us, data is powerful and data is valuable. So where there is a question of data, there is always a question of privacy trailing close behind. If we can imagine these technologies, we must also be able to imagine a future where our most intimate biological details are shared widely and accessible to many. The price of a detailed understanding of our own body is perhaps our privacy in that matter.
In this discussion, DeepMind are not strictly advocating privacy - rather, they are advocating transparency. Yes, your data will be accessed by many people, but with a strict record of who and for what purpose, which will ideally necessitate adherence to data sharing guidelines. Before patients themselves have access to their own records, this will likely still sit uncomfortably for many people. Until then, the success or failure of initiatives like DeepMind Health will determine how willing we are as a society to invest our data in our health, and to whom.


[1] http://bit.ly/2nfaDQ2
[2] http://bit.ly/1QM9PKF

by James Kerr, PhD Student AG Sterzer
this article originally appeared June 2017 in CNS Volume 10, Issue 2, Digital Health and Big Data