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hello everyone welcome to open specimen webinar we'll be starting shortly we'll just give couple more minutes for others to join okay we'll get started uh hello again
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this is purnima govindra from krishagnitrin i am the product manager for the open specimen i have with me colleen who will be doing a demonstration of implementation of open specimen in her bio repository uh i'll be starting with some introduction about open specimen we'll be recording this session so that we can share with uh other uh you know people who cannot uh attend today uh so we'll mute your lines uh if you have any questions please use the chat window we'll be having a question answer session at the
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end but please feel free to put your questions in the meanwhile on the chat okay uh so as i said uh this is the agenda i'll start off with uh just to give an a high level introduction about the product of course so the time won't permit to go into detail but you're free to contact us if you want a detailed demo but most of the time we'll give colleen to show how open specimen is implemented for there by repository we have been working with them for three plus years now and they use a lot of uh advanced features
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of open specimen and they are a very high throughput uh bank so it will be very interesting and uh good to understand how they have implemented open specimen okay so as i said you can use the chat window for questions we have been working with a lot of universities academic institutions hospitals and implemented open specimen for different use cases and for collecting samples across different bio banks or by repositories we are currently working with 70 plus customers across the globe as you see most of them are in us 70
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percent of our customer base is in us so like upmc in pittsburgh columbia university new york we have emory university of miami and of course university of maryland uh we have some client base in europe university of oxford university of basil and a lot of them also in australia and these
implementations range from enterprise version that is they have implemented at a university level uh where multiple bio banks are using single instance of open specimen or it can also be used for you know specific pi or research studies so it it
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can be at any scale we've also worked with a lot of customers for a very long time uh about 10 plus years like washington university is one of our biggest client uh they have 2 million plus samples and they have you know multiple studies across multiple groups you know almost 100 plus concurrent users using the systems extensively we also have instances in johns hopkins university of leicester singapore general health and university of new south wales in australia so we'll look at some quick product highlights and
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i'll move on to the demo uh so these are some of the main features of open specimen starting with
so there are very strict uh roles and privileges in place where you can control what the user can access and what they can do in the system using different roles and privileges and you can also manage different freezers so it can be any type of freezer maybe minus 80 freezers liquid nitrogen tanks or even room temperature cupboards where you
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store the tissue slides there are other features like you know handling collections across different types of studies it can be you know disease based or longitudinal studies or even just general biobanking studies which we call as collection protocols and in open specimen you can handle specimen data right from collection till the utilization so how the specimen is collected uh how is it processed where is it stored and all annotations related to open specimen that's why the whole life cycle of the specimen can easily be
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tracked in open specimen so recently we have developed two new modules which is e-consenting and mobile app which are for specific use cases but it is you know widely used now uh for uh you know some of the universities uh the system is hundred percent audit uh uh trial so anything that the user does starting from login add edit delete everything is audited uh and one of the favorite feature of open specimen is the powerful reporting tool so you can get the data out easily uh without you know depending on any i.
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t as such and of course finally it's a hundred percent rest api base which means that you can easily integrate with other systems uh so i'll also talk about some examples that we have integrated uh and one of the other priorities we gave during our releases is the scalability so as as i mentioned uh our clients have you know million plus samples so we don't want them to complain about performance issues so every release we make sure that there are priority given for any performance issues reported or performance
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enhancements so and as i said there is no issues when multiple concurrent users are using the system and we make new releases every three months and it is completely based on user feedback we get uh you know different uh from our different clients or users we get feedback and we try to incorporate them in the system so as i said we have done some integrations so these are some examples like red cap open clinica which are edc systems epic copac uh other custom in-house applications so this is if you want to pull data from
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you know other systems and you don't want to duplicate data entry so that you can do uh integrated reporting within open specimen we've also done integrations with equipments like automated freezers liquid handling systems in fact colleen would be talking about integrated integration with hamilton bios automated freezer uh so these are some examples of uh because of the rest api uh com compatibility so you you can integrate with multiple systems like this so that was a quick uh highlight uh we'll be i'll be showing some uh features in open
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specimen and then i'll be passing it on to colleen so this is a public demo site so any new user or anyone who wants to look at the re recent version of open specimen can go to
demo.openspecimen.org there is an evaluate button here so you can click and it will create like a sandbox for you so uh that way you can take a look at the open specimen so and if you see here this is right now v7.
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2 this is the latest version we plan to release in a couple of weeks and when so if you see here there are some graphs this is again an optional thing you can you know publish your data as a summary data to you know researchers where they can look at your biobank data at a quick glance so and these all these graphs and metrics are configurable using the reporting tool so let me go ahead and sign in so right now i'm logging in as a super admin and if i go to the home page i'll show you different features that can be accessible
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so this is the home page and since i've logged in as a super admin which is like i have access to everything i see all the cards but if you see roles there are different levels of access like administrator there is researcher technician tissue banker so if you see a specific role you'll
understand that you know the you can control different permissions at a very granular level like who can do read create update delete and different levels of permissions even in case of participant data who can access phi versus non phi that is who can
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access only d identified data all this can be controlled using roles and when you install open specimen there are default rules but you can customize these roles and once you have all the use roles in place you can create any number of user accounts and those user accounts will have some specific uh you know data about the user and then here is where you provide the roles so roles will uh let the user uh you know if you see here you every role is associated to a particular site so site can be uh you know anywhere the specimen
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is handled it can be hospital processing site or the site where the specimen is sent to so every user belongs to a site so this is how open specimen can work as a multi-tenant application where multiple users from different labs can use a single instance and you can still separate out the data that way and within the site you can have one or more collection protocols and within these two then you can provide a specific role and as you see you can also give multiple roles for a user so this is users uh let me show you
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how you can manage freezers so you can create any type of freezer there is no restriction on that and it can also show you like a hierarchy of the freezer for example this particular freezer has four shelves in it and each shelf has six five racks and when i click on the rack it will show me all the boxes within it so this one has 20 boxes and now i can drill down and see all the specimens within the box so this is a box and this is like a nine by nine box and these are all the specimens and these are empty locations
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i can click on any specimen to see what kind of specimen is it and all those so it's kind of like a graphical view of your freezer and you can define these freezers on your own you can have multiple freezers east freezers are associated to a site and you can track exactly where the specimen is stored yeah and as i said you can when you collect specimens you associate them to a collection protocol and this collection protocol can be of any type it can be longitudinal study disease based studies so as you see this
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is demo site there are different types of studies here and if i show you a particular study here so you can specify if you want predefined like a calendar for the study where you can specify what kind of specimens are expected to be collected how they are processed so this is like a one-time
configuration you do and once you set up in all these like users containers protocols which are administrative data which you do once in a while and once that is done then you can collect data so you can enter data about the patient
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so let me go into a patient here again from this screen onwards the data that fields that you see these are the default fields but you can configure the system to hide the fields that you don't need and you can add new fields very easily there is a custom form builder where you can add new fields to the database easily and here are some fields of the patient this is like a overview of one patient and these are all the visits that have already occurred i can go inside a visit to see what kind of specimens are collected
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how they are processed so if you see here this is a 60-day follow-up of this particular patient and there was a tube of blood collected there was plasma derived and these are the ali chords that were processed if you see these are all the specimen annotations or fields that you can capture like where is the specimen stored how much quantity was collected how much is still available what kind of specimen is it and all those details so there are many fields again based on your study requirements you can define uh what kind of fields that you need
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so these are all the data entry points so as you see there are multiple specimens collected in a time point and all these are tied to a patient and you can upload path reports you can upload any kind of forms data that is if you want to put annotation data or clinical data so all these are again optional things so let me now show the reporting so once you have all this data in how to get the data out so there is a reporting tool where you can do any type of reports so if i show you some default reports here so let me show you say this particular
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report so the way you create a report is you add filters so you can say give me all specimens of female gender patients so here if you see you can add conditions like this so let me add some conditions uh so if you see here it says that okay give me specimens collected between 2015 to 2016 there are where there are a liquid samples of a specific anatomic side suppose i wanted to offer one which belongs to lung so i all i need to do is add it as a condition like this so this way i can add any type of conditions and once i've added my conditions that
is filters to get the data out i can say get count it will show me how many patients and specimen match all these criteria that i have added so this criteria that you add it can be on any field of open specimen including any custom fields on including any fields that you integrate and get the data from other applications so you can add such filters now when i say view records it will show me a table view like this you can add any columns you want you can export it as a csv and any report you can save it for future use
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you can share it with others you can schedule reports and so on and finally if you want like a
summary based report you can do that as well so you can i'll just show you an example of a summary based report so if you see here this is showing me specimens of different studies across different studies than the type of specimens accounts so this is just a summary table instead of showing actual raw data you can also have such reports where you can create like pivot tables that you might use in excel so all such reports again can be saved
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and you know you can run it automatically on a scheduled basis if you want so that's the reporting and finally if you are giving the samples out out of your lab and you want to capture uh the data about who requested the specimens where did the specimens go out of the lab so all those are created as something called as orders so suppose i create click on this one this one was used for miami sponsor one study and this is the requester and it was sent on this distribution date and these many specimens were sent if
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you see this particular specimen it has been closed and it is distributed so this way as i mentioned you saw how specimens can be collected against a particular study and patient uh processed into alicorts at any level stored in freezers then finally you can use reporting to get specific specimens of interest and mark them as distributed which means that you're sending away for utilization of the specimens so these were some high level features of open specimen i know i was fast i was trying to you know squeeze in
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the main features within 20 minutes but if you are interested in a detailed demo of course you can contact us at any time and you can also look at demo site where you can you know play around and access the system to understand the features um so now i'll uh you know pass it on to colleen uh she's the director of university of maryland medical biorepository and we have been working with her since a long time and implemented open specimen they have multiple studies and uh let me pass on the sharing high quality
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[Music] thank you for inviting me to present today let me see if i can grab the screen from you okay okay are we able to see my slides yeah we can see it yeah okay great sorry i know that's on the zoom bingo card so i just had to throw that one out there so everybody can start their zoom bingo if you've seen that on facebook um so thank you for again for inviting me to present today as for nina mentioned i am the director of the university of maryland medicine biorepository just to give you a little more of my
background i've been here at the university of maryland for going on 19 years now i'm also faculty in the division of endocrinology diabetes and nutrition and my my training is in genetics human genetics i sort of fell into the biobanking role here at the university just based on the fact that we have so many samples from past studies in the amish which i'll describe a little bit later on in the presentation but we were sort of not organized as far as how we were handling those samples and at the same time that we realized
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that the program for personalizing genomic medicine was starting to come into existence and so the alignment of all of these biobanking necessities happened at the same time that i was there so that's sort of how i fell into it um just to give you a little background about the program for personalizing genomic medicine it's been here on campus for at least six years and what our role is is to advance the discovery of genomics and other homic sciences to accelerate trans translational research and implementation of
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these discoveries into more effective and safe individualized health care so basically the definition of personalized medicine and then we also have this education piece where we want to train health professionals and scientists and consumers in the great things that personalized medicine can offer so in helping facilitate that goal the mission of the umm biorepository is to provide the resources and support for large-scale studies to empower basic and clinical researchers to make discoveries in genomics and omic
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scientist sciences and to translate these discoveries to more effective diagnostics and therapeutics and the significance of our program is that we have this secured and managed environment for biospecimen processing storage and distribution which allows for multidisciplinary research that can impact a wide range of health issues it's also sort of a situation where we're getting to know the different researchers around the university so we can match people up in collaborations and that sort of helps move these research missions forward
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so as bernie was mentioning one of our our major resources for this effort is our state-of-the-art robotic freezer and liquid handling equipment we um we've been working with this equipment for probably the six years that we've been in existence um and we reached out to poor nema and stream early on because we just really needed a good way to organize ourselves and to be able to handle the large number of samples that we were planning to put into this robotic freezer other resources that we provide are of
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course trained laboratory staff dedicated to simple processing and management both that and our state-of-the-art equipment makes it um so that we can provide a more uniform and standardized um biospecimen processing process to our users so that you know a lot of clinical researchers don't have lab space they don't have the people that are available to make sure freezers aren't crashing on a saturday night so we can take those um stresses and those different responsibilities away from the researchers so they can focus on their
science and of course we have our highly configurable web-based biobanking informatics system for specimen annotation and management and we like to highlight to our users that there's an
investigator portal so i am i serve as a super admin for our open specimen instance but we set up user accounts for each and every pi and anybody on their research team using those user roles that pernimo pointed out earlier so that people can be proactive with their their specimen collection see what they have they can use the shopping carts to
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request samples from us request shipments to outside labs and that sort of thing we will talk more about that in a little bit we also have a software on campus called ilab that we use basically for billing of our customers um that one is very handy so that we're we're not doing journal entries or debit memos whatever your university calls it from one department to another um every month so we're able to make our financial system very smooth as well and then we also have a clinical research office that helps with
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regulatory expertise and provides support for studies that need somebody to quickly do some phlebotomy or well not quickly but you know what i mean um they help with irb submissions and it really helps to set people up for success in the biobanking arena so um i'm more on the laboratory side of things as i mentioned i'm a geneticist so my training is in lab so i leave the regulatory stuff to the people who are who are experts in that and and then i focus on the lab side so we do a lot of sample processing
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most of our samples end up being plasma and serum but we also do dna and rna extraction using our liquid handling instrumentation and of course we have short and long term sample storage at various temperatures from four degrees all the way up to the or all the way down to the vapor phase of liquid nitrogen and as prima mentioned we can manage the samples in all of these different freezers and refrigerators with open specimen and that brings us to the next bullet point um where where inventory management sample retrieval
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is is being managed through open specimen and of course i mentioned earlier we ship to outside laboratories we also have other word considered a core lab on campus so we also like to try and um cheerlead for our other core laboratories so we will make sure that people are considering other core labs when they have needs for their samples so this is the big granddaddy hamilton bios freezer it is an automated low temperature minus 80 storage system it is about the size of a small bedroom you can see my my now retired lab tech standing in
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front of the instrument so you can kind of get an idea of how big it is um and again we use this instrument for automated storage and retrieval of samples and as bernima mentioned we have an integration between the lymph system and the the bios so the restful api is used to integrate the two instruments or the two softwares so that they can talk to one another in general um the bios is not interested in who your patient is when the specimen was collected um how many times it's been frozen and thawed so open specimen can take care of
tracking that information for us and then basically they just share barcode information so open specimen will send information to the bios as we register samples and that information is a list of barcodes and the the bios uses that information to pre-register barcodes before we put the tubes and racks into the system and at that point we're free to enter the barcodes it's kind of a stop gap for us if we try to put a sample into the freezer that hasn't been pre-registered through open specimen it will um kick the the sample out
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and then we can track down why was this barcode um why was this tube entered into the freezer without being registered in an open specimen first so that helps us to really track and manage our samples very closely um this freezer will eventually accommodate over 900 000 samples so i can show you later how many samples we actually have in there we are i don't think to half of our capacity yet the freezer requires us to use these um particular tube racks in barcoded tubes and racks we use the 0.5 mil matrix tubes and we
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use the 1.5 ml nonq tubes you can see that they both have 2d barcodes located on the bottom of the tube and again these barcodes are used to track the sample from processing all the way through to entry into the bios and as well as retrieval from the bios when it's time to ship samples to someone so these racks the matrix racks hold 96 samples and the nuncracks hold 48 and there's actually a barcode a 1d barcode along this side of each rack so that the bios knows that can label a rack as well as the tubes inside it so it can
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[Music] locate the tubes when we ask for a sample pull using the open specimen so i just want to at this point show you a really quick video that might give you a better picture of how this process works it's a video that our pr department put together to help us because on the inside there's cutting-edge robotic technology to dramatically improve research efficiency a vast array of blood and dna samples can now be stored and recruited in minutes from a single secure location those
products will be things like serum and we extract dna 31:08
from the blood as well robots are also used to extract dna or labor storage in the biorepository this for a while we knew to extract dna primarily from blood samples that we can also collect from saliva muscle swab different types of tissues beam technology to move the dna from place to place while it's doing the extraction once the dna attaches to the bees it will go through a series of wash stuff so there are six wash steps that are going through you can see that the solution starts to clear off acid attached to the bottom of the magnetic
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rod so the advantage to using this machine is that we can get a dna each sample gets a unique barcode so that it can be tracked by computer and retrieved by the robots inside the cruiser we have here a sample rack with samples the 2d particulate examples i'll go through the barcodes on the bottom and then you can replace it and you'll do this and backup system stores the samples at ultra low temperatures we're inside the repository now where it's normally minus 20 degrees celsius but inside these cassettes where the
samples are stored it's minus 80 degrees celsius cold enough to a blister of human skin but no one needs to enter the freezer of the sample that's all handled by the roblox christian but human accurately retrieved hundreds or even thousands of related standards it is a huge fight and it's a huge improvement over traditional creatures with tubes that are hand labeled or labels of tape on the sides of the tubes and sometimes those labels come off it requires a lot of technician time the vital repository
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will eventually hold nearly one million samples all micro moments by the roblox to maximize the available space and retrieve samples in record time would be especially valuable to genomic
researchers the program for personalizing genomic medicine has set up a biobanking initiative in the hospital where collecting samples from any individual who walks through the door and is going to become a patient the university of maryland medicine bottle repository is a freezer that will be heating up research and discovery at the school of medicine
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so i just wanted to show that i think so you can get a clearer picture in your mind how the freezer works and um sort of what we're dealing with as far as the bar coding so take a walk with us so as i mentioned earlier we have a number of studies that we are maintaining using open specimen and the bios uh in the clip in the video clip i described a little bit about the um genetics biobank study which is the study that is funded and by the program for personalizing genomic medicine um we're collecting samples that can be
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used across the university anyone who is a university of maryland um investigator can write us an irb protocol to use samples for their purposes so we've set it up so that our irb consenting process is as broad as we possibly can while still protecting the rights of the human participants so for these for this study we have um collected dna plasma and serum for various biomarker studies and genomic studies we also have what we call the investigator-driven studies or i-drive studies these are investigators across the
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university who have their own study or their own project that they want to collect samples from we at this point have 42 unique pi's from 24 divisions that make up these 56 projects so some people actually have more than one project with us and we've collected anywhere from blood samples for serum plasma buffy code dna rna to saliva and buccal swabs for dna extraction we have a study collecting csf urine tissue cells all of these things if they can be frozen in those tubes we can bank them in the bios and for
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some investigators we have samples that we are tracking in manual freezers so many of these studies have studied specific data collection as well as connection to the electronic health record and as i mentioned earlier there's a lot of collaboration and sharing that has become evident through the work through the work of these investigators in the bio repository i also mentioned earlier that we have amish studies that we've been doing since alan actually started the first amish study with the with the lancaster county amish
back in 1995 and that was the amish family diabetes study so since then we've collected large cohorts for many other genetic diseases as well and we have um close to 10 000 participants with genotype and associated phenotype data in the areas of cardiovascular risk diabetes aging bone health and wellness and i will say that many of these samples are not collected in the tubes required for the bios so we are managing these in manual freezers and we're working on inventory doing retrospective inventory that we
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will eventually be able to upload into open specimen and one of the nice features about open specimen that will help us with this is that we can do a bulk upload so we don't have to put these samples in one tube at a time or one participant at a time we'll be building um excel files or csv files that will upload this information directly into collection protocols and with the specimen um this is just more information in the biobank samples i'll skip ahead so that we can get into the nuts and bolts of
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how we use open specimen so this is our our front page as bernina showed you when she before she logged in this is what our front page looks like i just wanted to show you this so that you can see how many participants work samples we have loaded into open specimen the primary samples would be sort of the parent collection samples and then these available specimens would be the aliquots of serum plasma you can see our our pie chart here that shows you know the majority of our samples actually aren't plasma and serum but
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some of these others are you know showing us a significant piece of the pie here we we had a large collection start at the beginning of the pandemic we have two two covid related projects that sort of kept us going during the pandemic when other research had to be closed down to some extent so we did the hospital did a healthcare worker antibody testing study and anybody who participated in that could consent to have a residual sample sent to us for for research purposes in the future so and the spirit of research our our
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health care workers did a great job and we have over 8 000 participants in that study and currently we are collecting specimens on totally positive patients who are in the hospital during various time points so that people can do longitudinal studies of their disease force while they were in the hospital so we've had quite an influx of samples over the last quarter but just to to show you our high level workflow we spend a lot of time working on our collection protocols making sure that we have them customized to each and every
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project that we do and the open specimen crew has been very helpful in times that i've needed them to help me build these collection protocols because i'm not a computer scientist in any way shape or form so i know enough to be dangerous and but at the same time open specimen is customizable and user friendly enough that i can work my way through building the majority of a collection protocol at this point and um i can turn it over to to to them to help me kind of make those larger scale um or higher maybe higher experience um changes to
the collection protocol to make sure it got it tweaked to its its best ability to to serve that particular project so collection protocols are very important in our and our use of the the product so once we have your samples stored collected and labeled properly including the barcodes that i keep talking about again we share a user account with every single pi so if and of course our pis are more or less interested in actually getting their hands dirty using open specimens so we will do um we will do sample polls
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just from an email from them describing what they want but sometimes our investigators will actually go in and build a cart and as as foreign showed earlier these queries that you can do in the reporting query and reporting module are great to help build these shopping parts of samples that people will want to pull or have you pull and ship to another laboratory and she was also describing how you set up a distribution protocol that can then refer back to a shopping cart to determine which samples need to be pulled
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and then of course at the end an order will be placed where the sample actually gets pulled so for us at the point where we um push the go button from a distribution protocol to an order that's when open specimen will tell the bios here's our list of barcodes that we want you to pull so we can set up a distribution protocol with the list of barcodes at four o'clock on our way out the door five o'clock on our way out the door i can set it up at home if i'm working from home and i can come in the next day and the
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specimen rock with the barcodes that i've requested will be waiting for me at the bios so um i used to know how many samples it could pull per minute or per hour but basically a fairly large size sample pool can be done overnight and it's ready for you the next day so you can pack it up and ship it before the fedex um before fedex closes for the day and then you're ready to roll with your sample shipment so this is sort of our high level workflow as i mentioned collection protocols are a big deal for us so i want to
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focus more on how the integration works when we are adding participants and specimens to our collection protocol so the integration actually involves this rapid data entry plug-in which allows us to register multiple study participants or visits at the same time as we enter their associated sample data and i'll show you what i mean by that when we go through an example as you can imagine entering each and every one of the barcodes in one of those tubes could get cumbersome so another great feature of the rapid data entry plug-in is that
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it allows for barcode assignment to full racks of samples so the 96 matrix or the 48 knob in one screen and it also feeds the sample barcode information into the integration of the bios as i
mentioned earlier that's our barcode pre-registration system so our workflow looks like this we can register patients a patient multiple patients or multiple visits for the same patient and during the patient registration the next step is to assign our visit details so is this a sample from a baseline visit a day six visit
a pre-treatment year one time point seven however you have your your collection protocol set up you can assign you can assign it this step what visit it is and then we move on to collect our primary specimens or the parent tube specimens so we consider our primary specimens would be our sst blood collection tube our edta blood collection tube or urine cup you know whatever your primary specimen is coming in we can assign the visit date and time at this point and indicate which primary specimens that we expected were
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actually collected for that participant for that visit at that point we can scan the two barcodes and as i showed you in the video we use um the thermo fisher scientific vision mate instrument to read our whole entire plate at a time so this software can show us the the barcodes across the whole 96 well plate or we switch to the 48 and they can read the number twos across the plate and then at that point we finish off by collecting our child specimens which means that we assign um our created on dates for our derived samples and our child
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specimens which would be the outbox and then we assign our freezer location for any score example so that could be assigning the alloplots to the bios or sometimes we when we would process the edta tube we'll spin it down take the plasma off the top to alipot and then we'll save the buffy coat and put it in q for dna extraction so those we actually store in a manual freezer so we can at that point say this tube went into this box in the manual freezer so that we can track where our dna samples are for our cube
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so at this point i wanted to just go into our open specimen instance and describe some of these things that i'm telling you on the slides so if we go into our collection protocols from the home page i have a particular study that i wanted to show you how we go through this process so we have the we have a bladder cancer by our repository if we open this up to the participant page and we want to add a new participant to our study then we can go to our rapid collection selection to begin adding a new patient so um at this point
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um we can register a new patient and let's say that today is the enrollment date you can enter some of the demographics about the patient we'll just make it up as we go and now we can register this patient and as i mentioned we have to now assign it a an event for the collection so this particular collection protocol has a baseline visit it has a follow-up blood or urine visit and it has a tissue collection so we'll just click on baseline for now and when we proceed to the next page this should be our collect
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our primary specimens page so our collection protocol is already set up to tell us which types of tubes we're expecting for this collection protocol or for this project so we're expecting to get a whole blood and red top a red tiger top a full blood and a lavender top and a urine sample and a sterile cup at this point you can assign the visit date and time and if you'd like to add a clinical diagnosis you can do that here as well so let's say that we collected all three specimens for this particular patient
so we move on to our scan our two barcode page so at this point we're going to see two boxes one is going to be the matrix box with the expected tubes so the one thing i left out is that when we're processing a sample we will assume that in a matrix rack we're going to use as many as 12 samples across one row so when we spin down one blood flexion tube we're filling as many tubes as possible across one row so here's our our serum our serum aliquots will be on row one our plasma aliquots will be on row two
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the rest of the rack will be empty we collect our urine samples and the note racks or the 48 setup wraps so here we collect as many as 10 urine samples across two rows of that rack so once we read our barcodes from the um from the scanner they'll show up in an excel file and what we can do is copy and paste our barcodes from here and i'm sorry go into our rack so in this case we had eight l clocks of serum six outer clocks of plasma these are all empty spaces and then for box two we can add in our our young two barcodes
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and in this case we we collected ten outboxes of urine so when we go to our next page this is where we can fill in information so here would be our primary specimen our collection date and time received date and time time this is our our position where we can add in the location of our tube that we're going to put in cube for dna extraction so this is our non-biospecimen um here are the derived specimens which are sort of the intermediary specimens once you spin down for me once i spin down a blood collection tube as my primary tube
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i assume that that unaliquoted um volume of plasma is my derived sample and then once i electrode that then it becomes my serum aloe box so as we showed before in the next last screen we had eight serum allopaths so now if we open this up we can see our barcodes for each of the outbox and when we assign our location it's going to be in the bios so these samples will then these barcodes will then be sent to the bios to pre-register these these tubes to come into the bios for storage so that's basically at this point we can
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submit this and it will populate the entire visit for this particular participant send the barcodes over to the bios for free registration and then at that point we can enter the tubes and racks into the bios and it will accept them as pre-registered barcodes and then we can assume that our samples are stored away nice and happy [Music] so i see them getting short on time so i won't be labor any more of the points here but just um to mention again that our biorepository the benefits to our users is that we can
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out they can outsource the management of their bio repository functionalities we have a regulated secure environment for biospecimen processing storage and distribution and 24 7 sample
monitoring and we have standard operating procedures for sample processing storage and heat and distribution and open specimen allows us to have a detailed biospecimen imitation tracking and reporting system and we have a dedicated expert staff that is eager to make sure that everything that is required for each ei study is is covered so here are
the contacts made for as the director of the buyer repository most employees can come to me kathy palmer is the head of our clinical research office who helps people with iob protocol issues and various other clinical duties here are the people that are integral to the development of the viral repository as well as the everyday um operations our funding comes through the program for personalizing genomic medicine and our instrumentation came from an nih shared instrumentation grant that was awarded in 2014 i think so we've been
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working with our instruments for quite some time now with that i can take questions um along with yeah uh thanks so much colleen that was very informative and uh very interesting to see how open specimen is used in real time especially high throughput biobank like yours uh so yeah anybody any questions uh comments please let us know let me also share my screen to show some of the resources we have uh so you can email us at contact open specimen auto rg if you have any questions or you need a customized detailed demo
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uh or if you want to just look at the software you can create your own uh
sandbox.demo.openspecimen.org and we have all our help manuals in help.openspecimen.org so if you want to look at some user manuals videos how to use the application you can access that it is publicly available okay any questions anyone okay so we have recorded this session we'll be sharing it soon uh thanks again colleen uh for taking the time out and explaining it uh so detailed and we really enjoyed it thanks everyone for joining in the webinar
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and we hope to talk to you soon again sometime thanks have a good day you
