Labii electronic lab notebook (ELN) and laboratory information management system (LIMS)

Saturday, June 6, 2020

Use Labii Scheduling widget to maintain social distancing while performing research

Starting in December 2019, a novel coronavirus (also known as COVID-19 or 2019-nCOV) swept across Asia, spreading to the United States by early 2020. By June 2020, nearly 2 million Americans had been infected and at least 100,000 coronavirus-related deaths had been reported. As orders to stay at home and close schools and restaurants spread, many research labs were also forced to halt their experiments and cease field work to protect scientists and follow local and state rules. 


But the world’s efforts to reduce the spread of COVID-19 appear to have worked. Data collected by Johns Hopkins shows that worldwide there are fewer and fewer cases confirmed daily. The question now becomes how to safely return to the workplace, especially to confined, enclosed places like research labs.  


According to the Center for Disease Control, one of the best ways to prevent further spread of COVID-19 is to stay at least 6 ft from other people, also known as social distancing. But social or physical distancing can be extremely difficult to maintain in small research labs, where several people may need to share the same equipment, or at least be near each other, to continue their work. 


To meet this need, Labii ELN&LIMS has an embedded Scheduling widget that allows researchers to not only schedule use of specific equipment, but to also schedule routine equipment maintenance, calibration, or sanitization. The widget is not limited to just equipment use; it can be used to schedule specific times for researchers to be in buildings or rooms like a lab or greenhouse. Schedules can also be viewed by other researchers that have access to the lab, allowing users to select specific times to do their work while following social distancing guidelines. Calendars can be viewed by day, week, or month, and entries are easily edited or deleted when your plans change. 


Scheduling widget at Labii ELN & LIMS



Most importantly, the Labii ELN&LIMS Scheduling widget allows you to continue important research while preventing the spread of COVID-19 and keeping your staff safe and informed.




Want to learn more? Schedule a demo today at https://schedule.labii.com.

Natalie Burger

Saturday, May 23, 2020

Why do I move away from zappa serverless?

There has been a lot of discussion on the use of serverless, especially with Zappa serverless. Based on my own personal experiences, I am here to summarize why I completedly shifted away from Zappa serverless after two years of use.

It is slow

Generally, with the lambda size of 1024MB, the API provided with Zappa is at least 10 times slower than some very basic EC2, for example, t3a.large. Even the t3a.small is faster than the Zappa.

It is difficult to work with SSO

If you want to integrate with SSO in Zappa, you are out of luck.  There are a lot of tedious configurations and it can not guarantee it is going to work. However, if you are using an EC2, the SSO works out of the box.

Here are some of the process I used to configure the Zappa to work with SSO:

  1. build a binary build from AMI
  2. copy `xmlsec1`, `libxmlsec1.so.1`, `libxmlsec1.so.1.2.20` to `/site-packages/lib`
  3. install libxmlsec1-openssl and copy `lbixmlsec1-openssl.so`, `lbixmlsec1-openssl.so.1`, `lbixmlsec1-openssl.so.1.20` to `/site-packages/lib`
  4. set `xmlsec_binary` in accounts/views.py to `"/var/task/lib/xmlsec1"`
  5. add `if modname != "saml2.extension.__pycache__":` to line 90 of the /site-packages/saml2/mdstore.py
  6. if metadata can not download, remove `public subnet` from zappa_settings
  7. if use slim_handler=true, add this code to zappa/core.py at line 408 to copy the `lib`. This need to be done whenever zappa is updated.
# code for step 5
def load_extensions():
    from saml2 import extension
    import pkgutil
    package = extension
    prefix = package.__name__ + "."
    ext_map = {}
    for importer, modname, ispkg in pkgutil.iter_modules(package.__path__,
                                                         prefix):
        module = __import__(modname, fromlist="dummy")
        if modname != "saml2.extension.__pycache__":
            ext_map[module.NAMESPACE] = module
# code for step 7
copytree(os.path.join(current_site_packages_dir, "lib"), os.path.join(venv_site_packages_dir, "lib"))

def create_handler_venv(self):
    """
    Takes the installed zappa and brings it into a fresh virtualenv-like folder. All dependencies are then downloaded.
    """
    import subprocess
    # We will need the currenv venv to pull Zappa from
    current_venv = self.get_current_venv()
    # Make a new folder for the handler packages
    ve_path = os.path.join(os.getcwd(), 'handler_venv')
    if os.sys.platform == 'win32':
        current_site_packages_dir = os.path.join(current_venv, 'Lib', 'site-packages')
        venv_site_packages_dir = os.path.join(ve_path, 'Lib', 'site-packages')
    else:
        current_site_packages_dir = os.path.join(current_venv, 'lib', get_venv_from_python_version(), 'site-packages')
        venv_site_packages_dir = os.path.join(ve_path, 'lib', get_venv_from_python_version(), 'site-packages')
        copytree(os.path.join(current_site_packages_dir, "lib"), os.path.join(venv_site_packages_dir, "lib"))

It could not load big sized data

There is a limit on the size of json the API can return with the Zappa serverless. This size might related to the lambda memory size you defined, but I have not tested. If you want your API to be 100% working even when querying a lot data, Zappa serverless is not for you.

It is difficult to debug

Recently I have problem to read the SSM with Zappa. It works well when you just deployed, but it will failed after 4 minutes, when a new session started. It looks like there are some consistancy problem for different sessions.

It is not cheap

Based on my calculation, the pricing of Zappa at the 1024M is similar to the a EC2 instance of t3a.large running 24 hours, at the pricing of RI. Almost no momey is saved.

Yonggan Wu

Friday, February 7, 2020

Labii ELN & LIMS facilitates infectious disease research

Labii ELN & LIMS facilitates infectious disease research
Scientist working on the BSL-4 Lab


Since it’s initial emergence in December 2019, the new coronavirus (2019-nCOV) has killed more than 600 people in China and infected over 30,000 people across Asia. The virus has now been confirmed in more than 24 countries, spreading from person to person through coughing and sneezing. The global effects of the coronavirus outbreak have spurred agencies like the World Health Organization to accelerate their research. Access to appropriate, safe lab space to study viruses like 2019-nCOV is imperative to understanding emerging health threats and developing effective vaccines and treatments. These spaces are called biosafety labs.

Most infectious disease research occurs in a biosafety lab to protect lab personnel, the environment, and other people from agents being studied. There are four levels of biosafety labs: BSL-1, BSL-2, BSL-3, and BSL-4. The Center for Disease Control and National Institutes of Health provide guidance for appropriate procedures and equipment based on the agent being studied. BSL-1 is the lowest safety level and applies to agents that pose a low risk to healthy adults. BSL-2 labs work with agents that pose a moderate risk to humans.

BSL-3 and BSL-4 labs work with agents that pose a much greater threat to humans, such as West Nile virus or the Ebola virus. At these biosafety levels, labs must take additional precautions to prevent microorganisms from entering or exiting the lab, such as non-recirculating air or high-efficiency particulate air filters. Even waste and water must be treated before exiting a biosafety lab at this level. As you can imagine, such strict policies can hinder a scientist’s ability to record their methods or results. Scientists in these labs wear a significant amount of protective gear, so traditional, physical lab notebooks are not an option.

Labii ELN & LIMS is an ideal solution for scientists working in a BSL-3 or BSL-4 lab. Research notes can be easily recorded on a computer inside the lab, ensuring methods and results are consistently and accurately documented. In addition, maintaining electronic records allows scientists to immediately share their findings, enhancing their ability to collaborate. Lab inventories can also be managed directly in Labii ELN & LIMS, allowing the user to track reagent and equipment use from outside the lab.

Want to learn more? Schedule a demo today at https://schedule.labii.com.

Natalie Burger